"There should not be a role for the European Court of Justice in any part of the UK, and that includes Northern Ireland," Javid told Sky News broadcaster.
As part of the Brexit agreement, there is no hard border between Northern Ireland and the Republic of Ireland, but under the protocol all goods and animal-based products coming from the rest of the British territories must be checked upon arrival in the UK province to comply with EU sanitary regulations.
Under such terms, the ECJ has the jurisdiction to oversee compliance with the protocol and to rule on disputes concerning EU law in Northern Ireland.
The UK government has argued that the protocol is not working, as it causes delays and interruptions to supplies moving between the UK and Northern Ireland.
On Wednesday, the EU said it could cut checks on food, plants and animals by 80% and paperwork for transport companies in half, but made no reference to the ECJ role, which according to Javid is one of "the most important issues" for the UK.
"I think that’s an over-legalistic approach that the court has. I don’t think that’s necessary," the health minister insisted.
Interviewed by Sky News shortly after Javid, Labour lawmaker and shadow international trade secretary, Emily Thornberry, said the Conservative government should not reject the EU’s proposal as "we can’t just continue to kind of keep kicking the can down the road."
"I think it’s probably a good basis for negotiations. We need to make sure that we have something which is permanent," she said.
The UK government said it was studying the EU proposal, but insisted on the need to make "significant changes" to the protocol.