Simon Dugdale, the director of communications at the Department for the Environment, Transport and the Regions, immediately took his annual leave but has not resigned from the Civil Service.
Mr Prescott has privately been critical of the way that his press has been handled after a series of attacks on his failure to deliver on the integrated transport strategy. He is said to have complained that the press campaign about his department's achievements has not been pro-active enough and the fightback strategy after negative reports weak and late.
"There is no shortage of achievements by the department but there has not been a proper press strategy to promote them effectively," an insider said last night. Colleagues of Mr Dugdale say he has been unfairly victimised and is the fallguy for controversies such as the M4 bus lane and the tension with Number 10 over the failure to deliver on transport.
His deputy Derek Plews said: "Simon Dugdale just decided to step down. He has been a head of communication in Government departments for 10 years and he decided that was long enough."
Mr Dugdale took control of the new super-ministry's press and communications division created for Mr Prescott after the May 1997 General Election.
He was one of the last heads of communication left from those appointed before Labour came into office. The most recent clear-out was at the Department of Health after Frank Dobson became frustrated with the failing press message. Andy Wood, former head of communications at the Northern Ireland Office, left after Mo Mowlam took over.
The pressure on Mr Prescott has intensified after public anger over GM crop trials, lorry-driver protests that choked London and a partial shut-down of London Underground, leading him to publicly recognise that he may be regarded as "unpopular".
His public profile was further damaged by the row with his father Bert who told newspapers how he doubted his son's claims that he was now middle- class. Mr Prescott fought back, telling of his childhood disappointment when his father did not buy him a bike because he had failed his 11- plus exam.
He also accepted that he found his stand-in performances at Prime Minister's Question Time difficult, but blamed Tony Blair's decision to extend them to a half-hour session, saying he found that purgatory.