Home Secretary John Reid has moved to scotch claims that John Prescott has been sidelined in anti-terror talks.
Mr Prescott was not at the initial Cobra meetings
The deputy prime minister is said to be "incandescent with rage" at press reports that he has been left out of the loop over the security scare.
Mr Prescott did not go to either of the initial meetings of the government's emergencies committee.
But Mr Reid said there was "nothing unusual whatsoever" in him chairing the Cobra meeting as home secretary.
More than 100 Labour MPs have also written a letter to Mr Prescott demanding Parliament be recalled from its summer break to discuss the Middle East crisis.
Mr Prescott, speaking on Friday afternoon, said "the efforts of everyone will continue".
"Next week, with my cabinet colleagues, John Reid, Ruth Kelly and Douglas Alexander, I will chair meetings here at No 10 with the Muslim MPs, other ministers from all departments and community leaders," he said.
Prime Minister Tony Blair is on holiday in Barbados but Downing Street says he is in "constant contact".
There was no indication that action was going to be taken "imminently" against the alleged terrorist plot when Mr Blair left the country, said Mr Reid - that had only become clear in the last 24 hours.
Mr Reid has chaired three sessions of the Cobra committee since late on Wednesday night and will head another meeting later on Friday.
Mr Prescott missed the first two meetings but attended the third.
At a news conference in London, Mr Reid said it was the "normal and conventional procedure" for him as home secretary to chair meetings about domestic security.
Previous home secretaries had chaired similar meetings which had been attended by Mr Blair and Mr Prescott, said Mr Reid.
"There is nothing unusual in that whatsoever," he said.
"Nevertheless, both the prime minister and the deputy prime minister remain fully briefed and fully involved throughout."
Mr Reid said the deputy prime minister was leading efforts to bring communities together in a "common purpose" against the terrorists.
'Knew what was happening'
On Thursday afternoon, the deputy prime minister joined Mr Reid and Transport Secretary Douglas Alexander at a meeting with the National Aviation Security Committee, which contains senior aviation industry figures.
Earlier, Mr Prescott's spokeswoman said he had been kept "fully informed" of developments.
"The deputy prime minister was being briefed face-to-face all night. He knew the Cobra meetings were taking place, he knew what they would be discussing," said the spokeswoman.
"He spoke to John Reid before and after the Cobra meetings."
Mr Prescott has also been briefing Cabinet ministers who are out of the country and MPs whose constituencies have seen police raids.
Last year, Mr Blair flew back from the G8 Summit in Gleneagles to chair Cobra meetings in the wake of the 7 July bombings - a task initially done by then Home Secretary Charles Clarke.
But a senior civil servant told the BBC News website that Mr Reid would have probably chaired Cobra this week even if the prime minister had been in the country.
The official said the home secretary usually headed meetings of the committee covering domestic security while the foreign secretary took charge when Cobra discussed international crises.
Downing Street says the prime minister has briefed US President George Bush about the terror arrests.
Twenty-four people are being questioned by police who say the alleged plot to attack passenger planes in mid-air could have caused "mass murder".
The Treasury has ordered the Bank of England to freeze the bank accounts of 19 people.
The Conservatives and Liberal Democrats have praised the government for its handling of the security scare.