The childcare subsidy returned to its pre-pandemic system on Monday, meaning parents again have to pay fees.

Payments were suspended in April after enrolment numbers plummeted with parents pulling children out of care because they couldn't afford fees or were worried about infections.

Small business ombudsman Kate Carnell says many families working in small businesses are relying on JobKeeper wage subsidies to keep afloat, which won't cover childcare fees.

"For small business owners - many of which are mothers - who have been working tirelessly to get back on their feet, childcare has just become unaffordable," she said on Monday.

"This could force parents - mothers more often than not - out of their jobs, which is detrimental to their business, their families and even worse for the economy."

Women have been the hardest hit by the pandemic.

Labor has also raised concerns about the impact on families but also childcare centres if parents can't afford fees any more and have to pull their children out of care.

"They saw it right to give relief for families in the last three months; my question to the government is what has changed?" opposition early childhood education spokeswoman Amanda Rishworth told reporters.

"The economy hasn't just gone back to normal, people haven't just walked back into their jobs."

Under the coronavirus relief package, the government paid its usual fee subsidy - worth about half a service's revenue - while parents paid nothing.

Most childcare operators were also able to get JobKeeper payments.

But Education Minister Dan Tehan said some providers had struggled with increasing demand for places while care was free.

Under the change on Monday, providers will get a transition payment worth a quarter of revenue. Wage subsidies to the sector end next Monday.

Mr Tehan said the subsidy had led to a seven per cent increase in women's workforce participation since it was introduced two years ago.

"We're confident that it will provide the support there for women, for single parents, and for all parents," he told ABC TV.

"I would say to all parents who have lost work or who have seen reduced hours, please get in touch with your provider to see what assistance is there for you."

Ms Rishworth said that help was only a small-scale program, supporting fewer than 1000 families.

With the average childcare fees about $120 a day, the JobKeeper or increased JobSeeker dole payments were quickly eaten up even with subsidies.

Ms Carnell called for the government to monitor the situation very closely and consider innovative ways to make sure women can stay in work.

Australian Associated Press