Visibility of American flag: The official Israeli reports say that the reconnaissance and fighter aircraft pilots, and the torpedo boat captains did not see any flag on Liberty. Official American reports say that the Liberty was flying her American flag before, during and after the attack. The only exception being a brief period in which one flag had been shot down and then replaced with a larger flag that measured approximately 13 ft (4.0 m) long. U.S. Naval Court of Inquiry finding number 2 states: "The calm conditions and slow speed of the ship may well have made the American flag difficult to identify." And finding number 28 states: "Flat, calm conditions and the slow five knot patrol speed of LIBERTY in forenoon when she was being looked over initially may well have produced insufficient wind for steaming colors enough to be seen by pilots". The NSA History Report (page 41) states: "... every official interview of numerous Liberty crewmen gave consistent evidence that indeed the Liberty was flying an American flag—and, further, the weather conditions were ideal to ensure its easy observance and identification."
U.S. crewmen's perceptions of intent: Surviving crewmembers of the Liberty claim that Israel's attack on the ship was "deliberate" and with full knowledge that the vessel was American. Israeli investigation and history reports agree that the attack was deliberate — but against what they believed was an Egyptian enemy vessel, not an American neutral vessel.
Distinctiveness of USS Liberty's appearance: One major dispute is whether the Liberty would have been immediately recognized as a different ship from the Egyptian ship El Quseir. Admiral Tom Moorer stated that the Liberty was the most identifiable ship in the U.S. Navy and in an interview with the Washington Post stated: To suggest that they [the IDF] couldn't identify the ship is ... ridiculous. Anybody who could not identify the Liberty could not tell the difference between the White House and the Washington Monument. Israel states in its inquiry and history reports that the identification as the El Quseir was made by the torpedo boats while the Liberty was enveloped in smoke and was based on "The Red Book", a guide to Arab fleets that did not include U.S. vessels.(Web site with images of both ships)
Identification markings: Liberty bore an eight-foot-high "5" and a four-foot-high "GTR" along either bow, clearly indicating her hull (or "pendant") number (AGTR-5), and had 18-inch (460 mm)-high letters spelling the vessel's name across the stern. These markings were not cursive Arabic script but in the Latin alphabet. Israeli pilots claim initially they were primarily concerned with ensuring the ship was a non-Israeli warship and that they ended the air attack when they noticed the Latin alphabet markings.
Ship's identification known during attack: A James Bamford book, published in 2001, claimed that secret NSA intercepts recorded by an American EC-121 reconnaissance aircraft indicate that Israeli pilots had full knowledge they were attacking a U.S. vessel. This 2001 proposition has played a significant role in the ongoing controversies about the incident, and continues to be widely cited. The tapes were later released by the National Security Agency in 2003 as a result of a Freedom of Information Act lawsuit brought by Judge and author A. Jay Cristol. However, instead of the EC-121 attack tapes requested by the FOIA request, the tapes released contained post-attack communications of Israeli helicopter pilots, their ground controller, and someone on one of the torpedo boats. The helicopters were sent to the attack site to provide assistance after the air attack. The helicopter pilots noticed an American flag flying from the ship almost immediately upon their arrival at the attack site and informed their controller. See other sources for a link to the NSA website with complete transcripts. The NSA Website denies that there are any U.S. recordings of the attack itself; although, this is disputed by several intelligence specialists who claim to have read the original transcripts.
Effort for identification: The American crew claims the attacking aircraft did not make identification runs over Liberty, but rather began to strafe immediately. Israel claims several identification passes were made. The Naval Court of Enquiry, based on the Israeli timeline of events, found "One may infer from the fact that within a period of approximately 15 minutes, the request was transmitted (for aircraft to be dispatched), received, a command decision made, aircraft dispatched, and the attack launched, that no significant time was expended in an effort to identify the ship from the air before the attack was launched."
Speed of the vessel: According to Israeli accounts, the torpedo boat made (admittedly erroneous) measurements that indicated the ship was steaming at 30 kn (35 mph; 56 km/h). Israeli naval doctrine at the time required that a ship traveling at that speed must be presumed to be a warship. A second boat calculated Liberty's speed to be 28 kn (32 mph; 52 km/h). The maximum sustained speed of Liberty was only 17.5 kn (20.1 mph; 32.4 km/h), 21 kn (24 mph; 39 km/h) being attainable by overriding the engine governors. According to Body of Secrets, by James Bamford, Liberty crewmen (including the Officer-of-the-Deck) and the Court of Enquiry findings the ship was steaming at 5 kn (5.8 mph; 9.3 km/h) at the time of the attack.
Commander W.L. McGonagle in his damaged cabin after the attack.
Motive: James Bamford, among others, says one possible motive was to prevent the United States from eavesdropping on Israeli military activities and monitoring the events taking place in nearby Gaza. In a study of the incident concluding that there was insufficient evidence to support either accidental or deliberate attack, Colonel Peyton E. Smith wrote of the possibility that "The attack was most likely deliberate for reasons far too sensitive to be disclosed by the US (or) Israeli government and that the truth may never be known". Author and former crew member James M. Ennes theorized, in the epilogue of his book Assault on the Liberty, that the motive was to prevent the ship's crew from monitoring radio traffic that might reveal Israel being the aggressor in its impending invasion of Syria, which the White House opposed. According to the Anti Defamation League "the argument that Israel knowingly attacked an American ship has always lacked a convincing motive".
Israeli aircraft markings: The USS Liberty Veterans Association says that the attacking Israeli aircraft were not marked, but a crewmember recalls watching a Jewish officer cry on seeing the blue Star of David on the planes' fuselages. (There are no international treaties governing aerial warfare requiring markings.) The torpedo boats that attacked Liberty did fly the flag of Israel.
Jamming: During U.S. Naval Court of Inquiry testimony, Wayne L. Smith, Radioman Chief, testified: "... We did have [radio frequency] jamming in my estimation. I was unable to determine this exactly, but every time it seems when an attack was made on us, or a strafing run, it was preceded by, anywhere from 25 to 30 seconds, carrier on our HICOM circuit, and I had ascertained to check this by calling the transmitter room and they said that they had not keyed the transmitter. This prevailed during the attack and quite a bit after the attack, intermittently." In a U.S. Navy message dated July 11, 1967, sent by Rear Admiral Kidd (senior member of Naval Court of Inquiry) via the Naval Communications Unit, Naples, Italy to Commander in Chief U.S. Navy Europe and Chief Naval Operations, Rear Admiral Kidd stated, in part: "Liberty reported apparent discriminate jamming on certain CW and voice circuits just before and during each aircraft's individual attack. Effect was to scare mischief out of those below who heard it start, because they knew a rocket or bomb would soon follow." None of the Israeli Defense Forces' investigations or reports confirm or deny radio frequency jamming was performed during or following the attack.
Visual communications: Joe Meadors, the signalman on bridge, states that "Immediately prior to the torpedo attack, he was on the Signal Bridge repeatedly sending 'USS Liberty U.S. Navy Ship' by flashing light to the torpedo boats." The Israeli boats claim to have sent the signal "AA" (general call) for which the formal reply would be TTTT later followed by both vessels sending identification codes. Commander Moshe Oren claims he thought Liberty signaled AA in reply, which was the same reply he received from the Egyptian destroyer Ibrahim el Awal eleven years earlier. Oren then consulted "The Red Book" (identification of Arabian navies) noting that the only match for the "old tub" with one funnel and two masts was the El Quseir. Meadors claims he never sent "AA".
Israeli ships' actions after the torpedo hit: Officers and men of Liberty claim that after the torpedo attack and the abandon ship order, motor torpedo boats strafed the ship's topside with automatic gunfire preventing men from escaping from below, and either machine-gunned or confiscated the empty life rafts that had been set afloat. The IDF claims that Liberty was not fired upon after the torpedo attack and that a rescue raft was fished from the water while searching for survivors.
Israeli offers of help: Claims differ about the Israelis offering help. The Liberty's captain and the Israelis both claim that help was offered, but at different times. The Liberty's Deck Log, signed by the captain, has an entry at 3:03 stating: "One MTB returned to the ship and signalled, 'Do you need help.' Commanding officer directed that 'Negative' be sent in reply." The captain testified before the Court of Inquiry, on page 40 of recorded testimony: "One of the boats signaled by flashing light, in English, 'do you require assistance?' We had no means to communicate with the boat by light but hoisted code lima india. The signal intended to convey the fact that the ship was maneuvering with difficulty and that they should keep clear." Liberty's logbooks (exhibits attached to Court of Inquiry proceedings) all indicate signal flags were raised at about 3:40 to warn the Israeli boats to stay away, the ship was "not under command." James Ennes, in his book about the attack, on pages 102 and 103, acknowledges the Israelis offered help, claims it occurred at 4:30, and the offer was rejected. The Israel Defense Forces's History Report about the attack, on page 19, claims help was offered at 4:30 and the offer was rejected.
U.S. rescue attempts: At least two rescue attempts were launched from U.S. aircraft carriers nearby but were recalled, according to the Liberty's senior Naval Security Group officer, Lieutenant Commander David Lewis. Lewis made an audio recording and later wrote about a meeting 6th Fleet Rear Admiral Lawrence Geis requested in his cabins: "He told me that since I was the senior Liberty survivor on board he wanted to tell me in confidence what had actually transpired. He told me that upon receipt of our SOS, aircraft were launched to come to our assistance and then Washington was notified. He said that the Secretary of Defense (Robert McNamara) had ordered that the aircraft be returned to the carrier, which was done. RADM Geis then said that he speculated that Washington may have suspected that the aircraft carried nuclear weapons so he put together another flight of conventional aircraft that had no capability of carrying nuclear weapons. These he launched to assist us and again notified Washington of his actions. Again McNamara ordered the aircraft recalled. He requested confirmation of the order being unable to believe that Washington would let us sink. This time President Johnson ordered the recall with the comment that he did not care if every man drowned and the ship sank, but that he would not embarrass his allies. This is, to the best of my ability, what I recall transpiring 30 years ago."