The Deputy Prime Minister publicly defied Mr Blair when he publicly expressed regret at the sacking of one of his closest aides in last week's ministerial reshuffle.
"I'm sad that Alan Meale's gone, he was a good minister, he did an awful lot for the reform of the waterways and changes in the department," Mr Prescott told BBC Radio 4. "But let's make clear - Prime Ministers make changes, they're responsible for Government."
Although Mr Prescott's tone was conciliatory, his defence of Mr Meale will be seen as criticism of Mr Blair, who moved four of the eight ministers at the DETR in an attempt to sharpen up its performance on transport.
Mr Prescott confirmed a report in The Independent last Friday that part of his Whitehall empire could be hived off into a new rural affairs ministry. He insisted he did not oppose the idea, expected in a White Paper on the countryside at the turn of the year.
"This isn't the first time this has surfaced," he said. "I have never set my mind against any kind of reflection and judgement to see how you can get better Government.''
Mr Prescott also confirmed he would be giving up a "hands-on campaigning role for the Labour party", saying he had suggested the move to Mr Blair eight or nine months ago.
However, Mr Prescott will head a summer campaign aimed at exposing the Tories as an "extremist sect". Labour will publish a series of reports on Tory extremism, in a dossier dubbed the "X files."
Mr Blair has written to all his ministers, urging them to throw their weight behind the campaign to highlight the dividing lines between Labour and the Tories.
Aides say he hopes last week's reshuffle will make the Government "more effective politically as well as administratively."
Mr Prescott said last night: "After just over two years, the Government already has a record of real achievements. In contrast, the Tories are floundering in opposition. They get more and more extreme with every policy they produce."