The timeframe for permanent facilities to operate the Irish Sea border has slipped by two years, a Stormont committee has been told.
They are now not expected to be built before 2023.
The agreement of the executive will also be needed, potentially complicating the process of approval.
Earlier this week it emerged that a Whitehall minister had written to the DUP's agriculture minister, telling him to get on with permanent buildings.
Edwin Poots has been resisting that, and a halt to work on the full-time facilities and staff to operate them has been ordered.
Checks are currently being run from temporary buildings in the various ports.
Tenders have been agreed for the work and it has emerged that compensation payments of up to £300,000 to contractors may be necessary due to the delay.
Earlier this year, MLAs on Stormont's agriculture and environment committee were told the planned facilities should be in place by June 2021.
Department of Agriculture, Environment and Rural Affairs (DAERA) permanent secretary Denis McMahon said the requirement to review the design and to get clarity on the potential volume of checks which may eventually be needed had pushed that back.
He said a business case for the £50m project would not be ready until October this year and the build would also now need executive approval as it was significantly cross-cutting and controversial.