HM Revenue and Customs (HMRC) has told businesses trading across the Irish Sea it will take a "sympathetic" approach to new customs rules in January.
Northern Ireland will leave the EU's customs union at the end of the Brexit transition in January.
However, it will enforce EU customs rules at its ports, meaning goods coming from Great Britain will need declarations.
HMRC estimates that will involve 11m declarations a year.
HMRC official Aidan Reilly told MPs on the Northern Ireland Affairs committee his organisation was "acutely aware" that many traders are going to be entirely new to these customs processes.
"We will of course want to be sympathetic to traders in the early days of the regime who are trying to do the right thing but are not clear on what exactly they need to do," he added.
The figure of 11m declarations was questioned by Alliance MP Stephen Farry.
He said industry sources in Northern Ireland found this figure "very, very low", and the a figure put forward by the Trader Support Scheme (TSS) was 30m.
The North Down MP said he was concerned if this figure was an under-estimation it meant some of the assumptions being made by officials were " off the mark ".
Mr Reilly said the number was "uncertain", while another HMRC official, Mark Denney, said he was "comfortable" with the figures.
The government set up the TSS to help Northern Ireland businesses.
It will help with the customs declarations, using a new digital system.
'Christmas is cancelled'
Mr Denney, said the necessary IT systems for trade between Northern Ireland and Great Britain would be "broadly functioning" by 1 January.
However, he said that some "external parties" were flagging that they "won't quite be there" so they were working with the TSS to provide additional help.
Mr Denney added: "Christmas is cancelled" for his team
He also explained that the main Customs Declaration System (CDS) is a "live system" but new functions for GB-NI trade are in testing.
He said there was a high degree of confidence in the system.
A second system, the Good Vehicle Movement Service, is '"fully built" and in testing with a major test due on 14 December
The issue of duty free sales at Northern Ireland airports after the transition period ends was raised by DUP MP for East Londonderry, Gregory Campbell.
He wanted to be assured the local airports would be given the same opportunities as airports in Great Britain and the Republic of Ireland.
He said senior staff from Belfast International Airport had written to Cabinet Minister Michael Gove about this issue.
It is understood that officials at Belfast International Airport have concerns that airports in the Republic of Ireland would be placed in a more advantageous position when it comes to duty free sales.
It is thought they have called for a duty free tax regime similar to the one used in Jersey.