Shimon Peres, the deputy prime minister, told Israeli radio: "Israel won't say, or not say, whether we have nuclear weapons."
"It suffices that one fears that we have them and that fear in itself constitutes an element of dissuasion."
During his senate confirmation hearing, Gates referred to Israel as one of the region's nuclear powers, along with Pakistan and Russia.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
The Jewish state is widely considered to be the region's sole nuclear weapons power, but has never confirmed or denied the suspicions, and continues to campaign against Iran's nuclear programme.
During the hearing, Gates speculated on why Iran might be seeking the means to build an atomic bomb.
"They are surrounded by powers with nuclear weapons: Pakistan to their east, the Russians to the north, the Israelis to the west and us in the Persian Gulf," he said.
The statement led Israeli media reports to suggest that the US may have breached a US "don't ask, don't tell" policy dating back to the late 1960's.
Binyamin Ben-Eliezer, a member of Israel's security cabinet, said in a radio interview "I haven't a clue why Gates made those remarks".
By not declaring itself to hold nuclear weapons, Israel also avoids a US ban on funding countries that proliferate weapons of mass destruction.
It can benefit more than $2 billion a year in aid from Washington.
This sanctioned reticence is a major irritant for Arabs and Iran, which argue the US is applying double standards in the region.
Analysts estimate that Israel has up to 200 long-range nuclear warheads.
In a documentary aired on Israeli television in 2001, Peres said that France agreed in 1956 to provide Israel with "a nuclear capacity" as part of secret negotiations ahead of the invasion of Egypt known as the Suez crisis.
Israel's nuclear programme came to the international fore in 1986, when Mordechai Vanunu, a former technician at the Dimona nuclear plant was kidnapped, taken back to Israel, and jailed after revealing the inner workings of the plant to Britain's Sunday Times newspaper.
He was released in 2004 after serving an 18-year term, but has been repeatedly banned from foreign travel.