The move by Mr Lyons to abandon the building projects at the ports was debated at Stormont on Tuesday.
The minister said: “A lot of people want to put their heads in the sand.
“We do face fundamental questions, we have fundamental concerns and challenges.”
Ministers from Sinn Féin, the SDLP and Alliance Party, the three pro-remain executive parties, contend that he does not have the authority to act unilaterally on issues considered significant or controversial.
Rival Stormont Assembly members have accused Mr Lyons of stunt politics.
He listed a series of problems with the protocol, including:
- Red tape and additional bureaucracy;
- Reduction in consumer choice;
- Problems facing hauliers transporting goods from Great Britain;
- Creation of barriers within the UK’s internal market;
- Businesses in Great Britain feeling they are not able to trade because of extra costs;
- Restrictions on livestock movements;
- Problems bringing guide dogs across the Irish Sea;
- Challenges transporting machinery.
Mr Lyons added: “It is so, so important that we get an alternative to the protocol.
“No amount of tinkering with it is going to make it work – it needs to go.”