The Department for Health has called on Secretary of State James Brokenshire to clarify how much funding it will receive, after MPs voted to pass a Budget for the region via Westminster.
The House of Commons unanimously backed proposals for the Budget bill, which has put in place financial provisions for Northern Ireland as local parties have failed to reach a deal to return to powersharing.
In it, Mr Brokenshire revealed an increase in health spending of 5.4%.
However, trade union Unison has argued this in effect amounts to a funding drop as it fails to keep up with health inflation which stands at 6%.
Mr Brokenshire told Parliament he will also release £50 million of funding for health and education, which will be the first portion of the £1 billion deal agreed between the Conservatives and the DUP as part of their "confidence and supply" arrangement to support the minority Government.
In a statement, a spokesman for Northern Ireland's Department of Health said: "It has to be emphasised that health is facing very significant financial pressures.
"The initial assessment of the financial position for 2018-19 and 2019-20 indicates pressures of some hundreds of millions just to maintain existing services.
"In relation to the secretary of state's comments on funding from the confidence and supply agreement, immediate health priorities would include investment in waiting list initiatives.
"Early confirmation of additional funding is essential as our ability to spend effectively diminishes with each passing week as we move closer to financial year end on March 31 2018."
Northern Ireland has been without an Executive at Stormont for 10 months, amid a powersharing deadlock between the DUP and Sinn Fein.
Despite numerous round of negotiations since powersharing collapsed in January, the parties have not been able to reach a deal to return to government.
The main areas of disagreement relate to language and culture issues including the implementation of an Irish language act.
Introducing the Budget at Westminster, Mr Brokenshire said he was reluctant to take the step but that Northern Ireland would otherwise run out of money by the end of this month without local politicians in place at Stormont to pass it there.
He added that he remains hopeful a deal can be reached between the parties, allowing a local Executive to still be formed.
