Gordon Brown has warned prison officers that delaying part of this year's public sector pay rise was "an essential part" of tackling inflation.
The prime minister said he would "do nothing" that put economic stability or low interest rates at risk.
Thousands of prison officers in England and Wales walked out on Wednesday.
They returned to work after ministers won a court injunction. The government and the Prison Officers' Association are due for talks on Friday.
An independent pay review body recommended a 2.5% pay rise but the government staged that rise, awarding 1.5% in April and the remaining 1% from November.
The Prison Officers' Association said it amounts to a second year of below inflation pay awards - and has not ruled out further strikes.
The decision not to award the recommended pay rises has angered many public sector workers, including nurses - who have also threatened industrial action.
But Mr Brown, who decided to stage the pay rises when he was chancellor, said: "We have succeeded in tackling inflation and having a stable economy because of discipline in pay over the last ten years. That discipline will have to continue."
He said staging pay awards was an "essential part" of controlling inflation, keeping interest rates low and creating more jobs.
"We will do nothing, nothing, to put that at risk. It is an essential element of maintaining discipline in the economy."
All 129 non-private prisons experienced some disruption on Wednesday, during a surprise walkout by about 20,000 staff, which was condemned by the government as "illegal" and "wholly unjustifiable".
On Thursday, Prison Governors' Association head Charles Bushell said that despite fears of disturbances, prisoners were co-operating with managers in getting jails back to normal.
"The governors I have spoken to this morning are saying that they have opened up cells as normal," he told the BBC.
"There is a lot of frustration among prisoners but it is being run off in the gym or fading away at normal courses or classes as life gets back to normal.
"While prisoners had a thoroughly uncomfortable day yesterday, locked up, with no advanced notice of the strike, their behaviour on the whole has been peaceful and good."
The Prison Officers' Association said the first national walkout in its 68-year history followed "two years of frustration and two years of below-inflation pay awards".
Its chairman, Colin Moses, said Mr Brown should "sit round the negotiating table" with them, as he had done with the NHS and Fire Brigades' Union.
"What Mr Brown wants to remember is, when he places 81,000 people in prison, he places them under the custody of my members, who are being assaulted on average eight times a day," he told the BBC.
"When we were awarded a 2.5% pay award by an independent pay review body - he staged it. Why? To drive down his economic growth? My members have had to take, as many other members of the public had to take, five interest rate (rises) this year on their mortgages.
"Go and tell a prison officer, who's facing the violence he's facing on a daily basis, that you're not going to give them any more - and he (Mr Brown) wants to ask why we can't recruit prison officers at the rate we should?"
For the Conservatives, the shadow work and pensions secretary Chris Grayling said Mr Brown was "heavily dependent" on unions to fund Labour.
"Growing signs of union militancy are a clear sign that they want something back from him in return," said Mr Grayling.