This answer referred to the original question as asked on 1 November 2017:
Why was the USS Liberty Attacked?
Why did the Israeli Defense Force attack the USS Liberty on June 8,
1967 killing 32 American Sailors, wounding 171, and doing so much
damage to the ship that it ultimately had to be scrapped.
The attack itself was conducted first by Airplanes, one of which
reportedly identified the ship to be American. Then by patrol boat at
close quarters. And finally, by helicopter.
Please support your answers and take into account the following US and
Israeli government statements on the attacks.
As stated on the Wikipedia page about the incident, both the Israeli and U.S. governments conducted inquiries and issued reports that concluded the attack was a mistake due to Israeli confusion about the ship's identity.
Since then, the NSA have released hundreds of declassified documents, including a report on the outcome of the Israeli Court of Enquiry in 1967.
A number of people, including surviving members of the crew of the USS Liberty, have certainly claimed that the real reason for the attack has been covered up by both governments. There have also been a number of books published on the subject, including Remember the Liberty!: Almost Sunk by Treason on the High Seas, by Ernest Gallo, Ronald Kukal, Phillip Nelson, Phillip Tourney, & Raymond McGovern and The Liberty Incident by Judge A. Jay Cristol.
However, as far as I am aware, to date nothing in the declassified records casts any serious doubt on the official story that the attack was a mistake, resulting from poor communication between units of the IDF and the mis-identification of the vessel.
In 2001, former Navy Chief Petty Officer Marvin Nowicki, who was the chief Hebrew-language analyst aboard a U.S. Navy EC-121 spy plane that was intercepting Israeli aircraft communications during the attack on the USS Liberty, stated in a letter to the Wall Street Journal that though he heard and recorded Israeli pilots’ and captains’ references to the U.S. flag flying on the deck of the Liberty, these remarks were made only after the attack was underway, and not before.
He stated that it was only when aircraft and motor torpedo boat operators moved closer to the Liberty that they were able to recognise, and therefore reference, the American flag.
Interestingly, Nowicki's letter sparked an investigation by the NSA who were concerned that the letter revealed classified details relating to US intelligence gathering capabilities. The existence of the NSA investigation was one of the details revealed among the classified documents leaked by Edward Snowden.