Parents said King David infant, junior and high school in Manchester telephoned them, sent invoices and kept a running total of "debts".
They said they faced humiliating inquiries into their financial circumstances if they did not pay, even though the small print on the invoices admitted that contributions were voluntary.
Now a letter to the school from the Department for Education and Skills has said governors must stop sending invoices and calling parents who have not paid.
It said the practices were "inappropriate" and asked for confirmation by next week that its procedures had been amended.
Ester Lyndley, a single mother-of-two who made the complaint, said: "The governors abused their power and intimidated parents. Education is supposed to be free, and that's that. No school should be allowed to ask for money."
Joshua Rowe, chairman of governors, said the school would continue to give parents statements showing any shortfall in their contributions and to make follow-up phone calls.
He said voluntary-aided schools needed to raise money to pay 10 per cent of their capital costs and for denominational education. Many such schools raise cash through religious institutions, but King David infants had no option but to go to parents, said Mr Rowe.
"If the DfES came and saw what we are doing here, they would find we are totally in tune with what they want," he said.
"We do not harass parents and we do not discriminate against them if they don't pay.
"But we will always ask parents, in a most reasoned and gentle manner, at least once a year if they can contribute."
The school could face a judicial review application if parents continue to feel under undue pressure.
* A security guard at King David school has accused Ester Lyndley of deliberately driving over his foot last month after an argument. Police arrested her on suspicion of assault a week later and released her on bail until May 12.