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Israel has arrested an Al-Qaeda-run militant cell in annexed east Jerusalem which was planning to bomb the US embassy, a spokesman for the prime minister's office said on Wednesday, according to the Voice of Russia.

The US State Department said it had been in touch with the Israeli authorities about the alleged plot but was not able to corroborate it independently.

"(The) Shabak arrested a terror cell from east Jerusalem that was operated by Al-Qaeda and planned, amongst other attacks, to bomb the US embassy," prime minister's office spokesman Ofir Gendelman wrote on Twitter, using the Hebrew term for the Shin Bet internal security services.

In a joint operation, the Shin Bet and Jerusalem police uncovered "a global jihad group from east Jerusalem which was operated from the Gaza Strip with the aim of carrying out major terror attacks in Israel," a Shin Bet statement said.

It said the attacks the group were plotting included bombing the US embassy in Tel Aviv, a double suicide bombing at Jerusalem's International Convention Centre, a kidnapping of soldiers from the city's central bus station and a bombing of a block of flats.

Two of the suspects - Iyad Abu Sara and Rubin Abu Nagma, both in their early 20s - were from east Jerusalem, while the third - Alaa Anas, in his early 30s - was from Jenin in the northern West Bank, it said.

The three were allegedly recruited online through Facebook by an operative in Gaza called Oraib al-Sham, who was connected to al-Qaeda, the Shin Bet said, without giving further details nor saying when they were arrested.

In November, court documents revealed that Israel had been holding a suspected Al-Qaeda activist without trial since 2010.

US State Department deputy spokeswoman Marie Harf said Washington was closely following the situation.

"Obviously we've been in contact with the Israeli government regarding these threats," she said.

"Obviously we're looking into it as well. I don't have reason to believe it's not true. I just don't have independent verification."

Harf said she did not expect the alleged plot to affect US-brokered peace talks between Israel and the Palestinians.

"We don't think this will in any way impact the peace process negotiations," she said.