The new 'Irish Sea border' is unlikely to be operational by 1 January, a think tank has concluded.
The Institute for Government (IfG) also said that the government should extend the Brexit transition period.
Under the Brexit deal, new checks and processes on goods being shipped from GB-NI should be in place by the end of the year.
Last week, the UK government published its approach to implementing the new checks.
The IfG said that move has come very late, given the amount of preparation still to be done.
Its report is based on interviews with civil servants, business groups and parliamentary staff in Belfast and London.
"By refusing to acknowledge publicly the existence or extent of the processes the protocol will involve until recently, the UK government has already lost valuable time," it said.
"It has failed to talk with business and other stakeholders to understand the implications of new requirements and help them prepare.
"Given the extent of the implementation task it is not clear that this work can be completed on this timescale."
'Risk of a hard border'
At the end of the Brexit transition period in January, Northern Ireland will continue to follow EU rules on agricultural and manufactured goods, while the rest of the UK will not.
Additionally, the whole of the UK will leave the EU's customs union, but Northern Ireland will continue to enforce the EU's customs code at its ports.
This will mean some new processes and checks for goods entering Northern Ireland from the rest of the UK.
The UK government can ask for an extension to the transition period next month but it is adamant it will not do so.
The IfG said that failure to implement the deal in time will have legal and reputational consequences for the UK, and economic and political consequences for Northern Ireland.
"A failure to ensure that the border is fully functioning when the protocol comes into force is likely to result in major trade disruption in Northern Ireland, and the risk that businesses in Great Britain cease trading with Northern Ireland to avoid legal risk - posing challenges for businesses in Northern Ireland," it said.
The organisation also called on the EU to show flexibility in implementing the new checks and processes if it wants to avoid the deal unravelling.
"Inflexibility from the EU could make arrangements overly onerous for Northern Ireland businesses, risking that the Northern Ireland Assembly will withhold consent for the continued operation of the arrangements for trade.
"This would reintroduce the possibility of a hard border - the very thing the protocol is designed to prevent."