Finance Minister Conor Murphy has met counterparts from Wales and Scotland to voice collective concern at the Internal Market Bill.
The powers enable the UK Government to undertake spending in devolved areas, including for replacement EU funding, without any engagement with devolved nations, Mr Murphy said.
The ministers also expressed worries about what this could mean for future funding arrangements.
Mr Murphy said: “The Internal Market Bill will give the British Government wide-ranging powers to make funding decisions in devolved areas.
“This is greatly concerning and could have huge implications for the Good Friday Agreement.
“The British Government should not interfere in funding matters which are currently the responsibility of the devolved administrations.”
He said Government should provide details on the scope of the Shared Prosperity Fund.
“This will be a vital source of replacement funding for devolved areas and the lack of meaningful engagement to date is extremely disappointing.”
The fund is designed to replace EU funds after Brexit.
The Internal Market Bill proposes to override parts of the EU Withdrawal Agreement relating to its provisions keeping Northern Ireland in the continent’s single market.