For the next school year, funding for a program that hires teachers to support children's learning recovery after the pandemic has not been approved.
This information was made public in a letter sent by the education minister to schools after term had ended.
Funding for a counselling program for primary school students is still to be confirmed.
According to a union, children are victims of inept politicians who fail to provide effective governance.
National Association of Head Teachers (NAHT), also stated that the Department of Education communication timing had been a source of "great offense".
In September 2020, the department introduced the Engage program. It will be continued during the 2021-22 school years.
Schools were allowed to hire substitute teachers and teachers in order to help students whose learning was most affected by the restrictions and pandemic.
Schools were awarded between PS3,600 to PS50,000 depending upon their size and the number of eligible students who received free school meals.
The funding for the Engage program was approximately PS15m for 2020-21 and around PS24m for 2021-22.
The department estimates that 600 teachers and 1,500 classroom assistants were employed in schools by 2021-22 to provide one-to-1 or small-group teaching to some students.
In the meantime, funding was provided by Healthy Happy Minds for counselling and therapeutic services in primary schools.
Primary schools used to have to pay for their own counselling.
During the coronavirus pandemic, there was a marked rise in the number of young people seeking treatment for mental disorders.
Schools also reported higher numbers of students with mental health problems, some "directly linked to lockdown".
Primary schools also had the opportunity to receive funding through Healthy Happy Minds to support their mental health.
Michelle McIlveen, Education Minister, wrote to principals of schools but was unable confirm that funding for the programs would be available in September.
She stated, "I have given a directive to my officials to continue these programmes until December 2022 in first instance."
"But, this direction is subject to approval by the Department of Finance.
"I understand the urgency of this issue. I can assure you that I will give clarity on budget allocations as soon I receive confirmation by the finance minister."
Before the Stormont Executive resigned in February, the Democratic Unionist Party(DUP) had not reached an agreement on a three-year budget draft.
The DUP has refused to nominate ministers until it addresses concerns regarding the Northern Ireland Protocol.
According to the NAHT, schools are "very concerned" by the uncertainty surrounding the schemes.
The NAHT stated in a statement that "the needs of our children is greater than ever" after the NAHT withdrew hundreds of millions from schools over the past years.
School leaders have felt great offence at the failure of the Department of Education communicate with their schools in a timely manner or with any clarity.
According to the NAHT, this has left principals unable plan for learning provision, and hundreds of teachers temporarily unemployed uncertain about their employment.
"It is therefore infuriating that our children, and school services, are again victims of the failure of our politicians in Northern Ireland to provide effective governance.
"Our politicians serve the public as public servants. They are elected by the people to serve.
"Using the most vulnerable members of society as leverage in a policy strategy has been wrong and will continue to be wrong."