Criticism continued as Mr Cook fielded questions in the Commons later on Thursday.
The Commons leader said Gwyneth Dunwoody, of the transport committee, and Donald Anderson, who headed the foreign affairs committee, were victims of the need to bring in fresh faces.
But, amid warnings of a backbench Labour revolt over the issue, he stressed MPs could force reinstatement of the pair if they wanted.
On Monday the Commons will have a free vote on the entire select committee membership list, rather than individual names, but changes can be proposed via amendments.
The sackings of Mrs Dunwoody and Mr Anderson provoked fury from all sides as ministers were accused of trying to reduce the independence of parliament and scrutiny of their work.
Quick move
But Mr Cook, the former foreign secretary, said the government had moved to ensure this parliament's select committees were up and running "in the fastest time" ever.
"This will mean that they can meet next week, they can choose their chairs, they can start to look at the programme of business, if they want they can meet during the recess," he said.
"I have given them more freedom, more discretion.
He also pointed out that individuals not known as government loyalists, including David Hinchliffe, ex-minister Chris Mullin and the "terrier"-like Andrew Mackinlay, had been nominated for appointment to select committees.
Downing Street later distanced the prime minister from the sackings.
Party matter
Tony Blair's official spokesman said it was largely a matter for the party and Mr Cook.
But it is not yet clear if Mr Cook's assurances will placate MPs angry at the sackings.
Labour's Tam Dalyell - as the longest serving MP now Father of the House - said: "It does look as if they're wanting to avoid awkward chairmen of awkward committees asking awkward questions."
And that, he went on, raised the crucial question of whether the Commons was a scrutinising body or just "a pool of talent for the executive".
Rebellion risk
A backbench revolt on Monday was "possible but not probable", he added.
Another Labour MP, former arts minister Mark Fisher, said it made "absolutely no sense" for ministers to appoint and set up their own invigilators and he warned: "This won't blow over."
Criticism continued as Mr Cook fielded questions in the Commons later on Thursday.
Conservative MP Eric Pickles declared of Mrs Dunwoody that "there is more vitality running through her veins than many of the yes men and women that seek to replace her".
Mrs Dunwoody became known for her attacks on Railtrack and government plans to part-privatise air traffic control.
Saying she was "very disappointed" at her removal, she warned: "The (transport) problems will continue and they won't go away by chopping off the head of criticism."
Mr Anderson oversaw critical reports from the foreign affairs committee covering issues including the arms-to-Sierra Leone affair.
He expressed disappointment at his removal and called for select committees to continue "keeping the government on its toes".
Select committees are cross-party bodies whose role it is to scrutinise the work of government departments.