George Eustice told MPs there were around 1,000 officers able to issue export health certificates for fish, although Westminster is working with its Scottish Government counterparts to help fill a "gap" in Scotland.
Speaking in the Commons, SNP MP Richard Thomson (Gordon) said this week's test run for border procedures once the transition period ends demonstrated the "severe chaos" that might be expected in the new year.
He stressed the need for seafood products to be delivered to market at speed, adding: "What assurances can the Secretary of State make today to the catching and processing sectors that delays will not equal ruined produce and ruined businesses?"
Mr Eustice replied: "We've been working with the fishing industry and local authorities to ensure they have the capacity in place to employ the environmental health officers necessary to issue both the catch certificates and the environmental health certificates.
"We have around 1,000 officers now that can issue export health certificates for fish.
"It is the case there are some concerns in Scotland where the Scottish Government potentially has a gap in capacity of 100. We're working with them to try to offer our help to ensure this gap can be filled."
For Labour, shadow environment minister Daniel Zeichner asked Mr Eustice to explain his plans to keep "our food supplies flowing" in 35 days when the Brexit transition period ends.
Mr Zeichner said: "Mr Speaker, 26 per cent of our food comes from the European Union and it's reported that last week Defra's head of food security warned industry reps to expect just 40 per cent flow rates."
Mr Eustice said the UK Government had been working with the industry to ensure the capacity was in place to issue export health certificates, adding: "Of course we continue to work on plans to ensure that goods flow at the border."
He earlier stressed the UK had offered the EU a free-trade agreement which would involve "zero tariffs on all goods".
The Environment Secretary was also challenged about comments he made on sheep farmers, to which he replied: "I never said that specialist sheep farmers and crofters should diversify into beef.