Downing Street yesterday shrugged off the revolt by 31 Labour MPs against the introduction of student tuition fees and the abolition of maintenance grants.
But the Deputy Prime Minister sounded a note of concern in his exclusive interview with The Independent about the party. He believes Labour spokesmen have succeeded in making the step from Opposition shadows to ministers in charge of Whitehall departments, but the party has yet to get right the shift from Opposition to government.
"I think that has yet to be sorted out and it is the very area where the interface between the party in Opposition, and the party in government is most felt. I don't think we have got that any where near right as it should be.
"There are changes in the general secretary and the rules. That is an area I am a little nervous about. I don't think we have got the framework near right yet," said Mr Prescott. "I'm saying it's an interface between Opposition and Government.
"We have all had to go through it, from MPs to party staff. I think that is a process which we haven't examined enough and yet the manifestations of those sensitivities are all around us.
"The relations with the PLP and with the party. I think in the coming year as Deputy Leader I will need to live up to what I think the Deputy Leader's job is."
He had his 60th birthday last week and he says that in the past 10 years of his political life, he has no intention of fighting frustrating battles over whether he should be the one to sort out relations between the party and the Government.
The Deputy Prime Minister confirmed he would be voting for Dennis Skinner against a whips' slate of three candidates in the elections to the party's National Executive.
That will be seen by the MPs as a signal to ignore the whips' pressure in the secret ballot, but his weekend message was clear: if the Prime Minister wants him to do so, he is ready to increase his workload over the next year to quell some of the unrest.
Last night, the revolt over student grants and tuition fees ended with the third reading of the Teaching and Higher Education Bill, but the discontent rumbled on with Labour backbenchers complaining the guillotine had limited their scope to air their grievances.
David Blunkett, Secretary of State for Education and Employment, defended the Government's position over tuition fees, saying that he thought it was right that students should be expected to make a contribution.