The judge also said that given recent violence in Northern Ireland attributed to opposition to the protocol, it was incumbent on political leaders to be seen to be upholding the law.
Belfast businessman Sean Napier has already secured a court judgment that declared the DUP boycott as unlawful.
However, that ruling has not prompted a change in the DUP policy of non-engagement.
Napier’s lawyers sought a further ruling compelling DUP first minister Paul Givan to engage with Sinn Fein deputy first minister Michelle O’Neill and the Irish government to set a date and agenda for the next plenary meeting of the NSMC.
It cannot happen without the participation of the DUP and the party is currently not engaging in the cross-border political structures set up under the Good Friday agreement, with the exception of meetings related to health issues.
The party contends that the Brexit protocol and its associated barriers on Irish Sea trade have damaged east/west relations and, as such, it should not be business as usual when it comes to north-south relations.
Mr Justice Scoffield refused to grant the mandatory order against the DUP ministers, but reaffirmed his earlier declaration that their policy was unlawful.