"Here, several years ago, in the situation room of the ministry of foreign affairs, we dealt with a siege that grew ever tighter around our people in the Israeli embassy in Cairo," he told an annual memorial ceremony for ministry staff killed on duty overseas.
"A wild mob came to slaughter our people and that night we worked with all the tools at our disposal, including threats to extract them using the Israel Defence Forces, which finally tipped the scale," his office quoted him as saying in statements issued in Hebrew and English.
It later issued what it called a "clarification" saying that the premier's remarks did not mean he was speaking of unilateral action.
"In the circumstances referred to, the intention was to act in coordination, with the Egyptians, not unilaterally," it said.
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"We are happy that there was no need for this and we thank the Egyptian army which dealt with the crisis in a responsible manner and brought about a solution to the problem."
In the September 2011 siege, protesters attacked the Israeli embassy offices in central Cairo, forcing the evacuation of all staff.
Crowds smashed through an external security wall, tossed embassy papers from balconies and tore down the Israeli flag.
After several hours, Egyptian commandos rescued six Israeli security guards stuck inside the embassy building.
It was the worst such incident since Israel set up its mission in Egypt, the first Arab country to sign a peace treaty with the Jewish state, in 1979.
Ambassador Yitzhak Levanon was among 80 embassy staff and their families flown home early the next morning. The six guards followed later.