It was a case of mistaken identity, according to  the Israelis. It happened during the Six Day War, the IDF/AF were taking out any and all enemy ships and planes to prevent an attack on them. \n\nIsrael paid $13,000,000 in indeminties to the US and lodged a formal apology. \n\nHowever the incident is slightly shady, since the American ship did not look at all like an Arab ship, and it was also an intelligence vessel.\n\nThe reason it got covered up is obvious. One, its an intelligence vessel. The press loves finding intelligence gaps, and losing a ship like that is an embarresment to the US. Two, it could badly damage US-Israeli relations, which werent strong then but were now. That's probably why this story took so long to get out.\n\nto the other guy who answered, you are thinking of the USS Cole, which was attacked in Yemen and was not covered up. The terrorists responsible escaped from a Yemeni prison.