The USS liberty was a SIGINT vessel under the command of the Sixth Fleet commander at the time of the attack. This information is supplied in the documents released by the NSA. The majority of the complement of the USS Liberty were US Navy. There was a small complement of three or four civilian technical personnel.
According to the immediate report the Israeli government claimed that the attack was made in error and they "apologised abjectly". Based upon the information I have read on the attack this was pure hokum and the Israelis knew perfectly well that it was a US Navy intelligence gathering vessel that had been despatched to the area on June 2, 1967 in order to monitor any military activity in the area due to the worsening situation. (This is also mentioned in the documents you linked to.) It is reasonable to assume given their record that they had been informed of the USS Liberty's mission by one of their spies in the US government. It is likely that they wished to prevent any monitoring of their actions that could be used in pursuance of war crimes prosecution.
Here is an excerpt from the immediate report (sic):
"After talking to Mr. McNamara, Captain Thomas called and advised the Director the.t he had confirmed the information 1ll1ready furnished Mr. McNamara and that he had reported a cOIl\Plement of 15 officers and 279 enlisted men, of Which the SIGINT Detaohment was siX officers and 128 enlisted men (the latter figures ware initially reported to Mr. McNPlara as comprising the total complement of the ship by someone in the pentagon).
When Mr. McNamara asked about the ship's function, Captain Thomas replied quoting the unclassified mission statement, nconducting tec}m1cal reltearch operations in support of U.S. Navy electrcmaqnetic cOll\lll\Uliclltions and advanced communications *ysteme to include .atellites." Captain Thomas also reported that the ship had departed Rota, Spain, on 2 June."
"Jesus answered them: 'Truly, truly, I say to you, everyone who commits sin is a slave to sin. The slave does not remain in the house forever; the son remains forever. So if the Son sets you free, you will be free indeed.'" (John 8:34-36)
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