HMRC boss John Thompson also said a new customs arrangement with the EU could cost as much as £800m and take seven years to implement.
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But he said there had been “extensive conversations” with the Treasury.
Mr Thompson said HMRC was investigating the “business case” for a new Singapore-style system, which would allow firms to get their tax and border checks done in one place.
This would bring together 26 different organisations into a “single window”, and make trade “much smoother”.
However, he said the undertaking would be a “mega project”.
“We need to be transparent with you… You need to be thinking about that as a project that costs somewhere between £500m and £800m,” he told MPs.
“It would take five to seven years to implement,” he said.
Another HMRC official told the MPs the agency would have to deal with an additional 130,000 new companies after Brexit.
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