Northern Children's Network general manager Maggie Wilson said the sector was caught on the back foot by the Prime Minister's announcement of free childcare.
Early childhood education centres have been in a state of uncertainty with many parents choosing to keep their children at home during the coronavirus social restrictions.
The federal government announced it will start making payments to early childhood education centres at the rate of 50 per cent of the fees they were receiving in February. Parents who continue to use the services will be able to do so for free.
But Ms Wilson said despite needing to transfer onto an entirely new operating system by Sunday night, they still did not know exactly how the changes would work.
"It was a shock because we found out alongside everyone else, and we had families and educators calling up to see what it meant for them, and we didn't have the answers," she said.
"But it means that families can now re-enrol and be on the books whether they want care during these crisis times or not. It's definitely a win-win, but we've got a few weeks of struggling through."
Glen Dhu Child Care Centre owner Mel Reid said the government stepping in with 50 per cent of their pre-crisis revenue would not be enough to keep her business viable.
"We aren't breaking even," she said. "That's really devastating."
"We can not remain viable in the current state things are in. [The announcement] sounded great, and I did shed a tear that we were listened to. But then boom, boom, boom - the more I read the fine print, the worse it got, and then I was crying tears of distress.
"This is a business I've had for 23 years here, rated on the highest possible accreditation, having a moral obligation to keep my doors open for those families that need it, and not being viable."
Both Ms Wilson and Ms Reid said a major problem facing the sector was that their revenue had precipitously declined since the start of March, but the Jobkeeper wage subsidy does not come into effect until early May.
"How can I say to my educators, come in, even though we can't give you any money?" Ms Reid said.
"We still need money in our reserves to pay staff until it comes in," Ms Wilson said. "So we've still got five weeks to go, and it's great to see families come back and re-enrol, that made us feel good. But we've got a long way to go to see what the financial repercussions are for our organisation."