Moshe Yaalon was quoted as saying that John Kerry was acting out of “misplaced obsession and messianic fervor”.
The US state department expressed anger at the remarks.
However, in a statement, Moshe Yaalon’s office said that he had no intention to cause any offence.
“The defense minister… apologizes if the secretary was offended by words attributed to the minister.”
Israel and the US shared “a common goal” of advancing peace talks with the Palestinians, the statement said.
“We appreciate Secretary Kerry’s many efforts towards that end.”
The White House said the alleged comments were “inappropriate” given America’s support to Israel’s security.
It was a rare rebuke to America’s ally.
Moshe Yaalon’s alleged comments – first published by Yediot Ahronot newspaper – may reflect the mind-set of other government officials, but Israelis want to protect their relationship with their strongest ally.
The minister said a security plan that John Kerry had presented to Israel was “not worth the paper it was written on”.
“John Kerry – who has come to us determined and is acting out of an incomprehensible obsession and messianic fervor – cannot teach me anything about the conflict with the Palestinians,” he was quoted as saying.
Moshe Yaalon expressed the hope that John Kerry, who has made 10 trips to Israel since March, would terminate his drive for peace and focus his energies elsewhere.
“The only thing that might save us is if John Kerry wins the Nobel Prize and leaves us be,” he was quoted as saying.
Moshe Yaalon made his comments in private conversations in Israel and the US, the Israeli newspaper said.
White House spokesman Jay Carney accused the minister of misrepresenting John Kerry’s proposals.
“Secretary Kerry and his team have been working non-stop in their efforts to promote a secure peace for Israel because of the deep concern the United States has, and the deep commitment the United States has for and to Israel’s future and the Israeli people.
“To question his motives and distort his proposals is not something we would expect from the defense minister of a close ally.”
Moshe Yaalon’s comments also drew criticism from PM Benjamin Netanyahu.
John Kerry has in recent months attempted to inject momentum into Israeli-Palestinian peace talks re-launched last July.
But the talks have so far shown little sign of progress.
Earlier this month, he held talks with Israeli and Palestinian representatives in an effort to secure a “framework” for a final Israeli-Palestinian peace agreement.
However, Israel is said to be demanding that it maintains a military presence under any future peace deal with the Palestinians.
While the peace talks have been continuing, Israel last week announced plans to build 1,400 new homes in Jewish settlements in the West Bank and East Jerusalem.
A dispute over settlement construction led to the collapse of the last peace talks.
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