The acknowledgment by the unnamed official Thursday also followed a false cover story from Netanyahu's military attache that Netanyahu had visited "security facilities" in Israel Monday during an unexplained absence of more than 12 hours.
Israeli media initially reported he had toured a facility belonging to the Mossad national intelligence agency.
But then Israeli daily Yedioth Ahronoth reported Netanyahu had, in fact, flown secretly to Moscow to express concerns about the possible sale of Russian anti-aircraft missiles to Iran.
"There were many considerations, many reasons, that the prime minister's schedule on Monday was not made public," an unidentified Israeli official told The Times of London.
"It was in the interest of national security, which has now been damaged by these leaks," the official said.
The visit appears linked to the Russian cargo ship Arctic Sea, reported to have been carrying wood, that was reported seized by pirates July 24 as it passed through Swedish waters, The Times said.
Russian Foreign Minister Sergei Lavrov Tuesday denied the ship had been transporting an illegal shipment of S-300 surface-to-air missiles destined for Iran, calling it "is an absolute lie."
Netanyahu has not responded directly to the reported secret trip.
In Moscow Thursday, Russian Foreign Ministry spokesman Andrei Nesterenko told reporters when asked if the meeting took place: "I am not saying yes or no. I am just saying I don't have any information."