The ferry company, which runs services from Portsmouth, Poole and Plymouth, was given the grant to help it comply with new EU regulations.
The grant will be used to fit "scrubber systems" on the exhausts of three of its ships to reduce sulphur emissions.
A company spokesman said it was "a welcome contribution" but only covered about 8% of the total cost.
Three of the company's ferries have already had the modifications, which are an alternative to converting them to use more expensive marine diesel.
The regulations on sulphur pollution came into force in January.
Brittany Ferries has received almost £5m from the European Union (EU) to pay for low-emission exhaust systems.