Deputy Labor Leader Tanya Plibersek says the agreement that's been rolling since 2008 won't be extended beyond its current end date.
"That means Australian children will be educationally disadvantaged," she told reporters in Sydney on Tuesday.
But the government denies that's the case and says it's working on the next agreement with states and territories.
It wants to see co-operation from all levels of government to improve preschool attendance rates, with 30 per cent of children currently attending fewer than 15 hours a week.
"Extending the national partnership gives us time to work through these attendance issues with the states and territories," Education Minister Simon Birmingham said.
The government wanted to ensure that beyond 2019 children were not just enrolling, but attending and benefiting from preschool programs in readiness for school, he said.
A report by the Mitchell Institute at Victoria University has warned it would be "extremely dangerous" if a new agreement wasn't in place for 2020 onward.
Director Megan O'Connell said without preschool more children would start school when they're not ready, putting more pressure on teachers and leading to more struggling students.