The Northern Ireland assembly has voted to continue with the special Brexit trading arrangements for another four years.

It means Northern Ireland will retain some EU trade laws as a means of maintaining an invisible border on the island of Ireland, despite continued opposition in some unionist quarters.

The 48 votes to 36 ballot reflected the long-held divisions on Brexit, with unionist members of the legislative assembly (MLA) voting against and the nationalist and the non-sectarian Alliance party supporting it.

The Northern Ireland secretary, Hilary Benn, confirmed he would proceed as required by the law, including to commission an independent review of the functioning of the arrangements.

“The government remains committed to implementing the Windsor framework in good faith and protecting the UK internal market, in a way that offers stability and works for Northern Ireland, for businesses, and for traders,” he said.

It came after almost five hours of debate, described by Social Democratic Labour Party MLA Sinéad McLaughlin as “triggering”, with a retread of the Brexit points from unionist benches.

Under consideration was the continued application of articles 5 to 10 of the Windsor framework, which centre on customs, movement of goods, VAT and excise duties, the single electricity market and state aid.

Emma Little-Pengelly, the deputy first minister, said the DUP would “continue to fight to fully restore Northern Ireland’s place within the UK”, including the removal of the application of EU law and any barriers it creates in the internal market of the UK. “We need to strive for something better,” she told the assembly.

The Alliance party’s Naomi Long, the justice minister, said it helped no one to allow Brexit to be a “constantly open wound” and she would vote to retain the arrangements to allow NI to “move forward”.

Matthew O’Toole, leader of the SDLP in Stormont, said the protocol was imperfect but urged members to look forward. “There needs to be a focused effort on improving things,” he added.

This prompted the Ulster Unionist party’s Steve Aiken to say the “strongest message” to Brussels and London was to unite behind a vote against the Windsor framework continuing.

Tuesday’s vote was the first test for the compromise deal struck by former prime minister Rishi Sunak and the European Commission president, Ursula von der Leyen, in February 2023.

The DUP’s Jonathan Buckley called the vote “an illusion of democracy”, with London the ultimate arbiter of what laws prevail under the trading arrangements.

The framework was brought in after protracted opposition by the DUP and others over checks on fresh farm produce, ranging from sausages to cheese, being brought into the region from the rest of Great Britain.

Under the Windsor framework, goods from Britain destined to remain in Northern Ireland travel through a “green lane”, with a separate “red lane” for goods destined to go over the border into the Republic of Ireland and therefore the EU.

Bans on the import of seed potatoes and 11 native British trees were also lifted, as were EU rules on moving pets from Northern Ireland to Britain.

Keir Starmer has said the Windsor framework is the only viable basis for stability in Northern Ireland.

In “explanatory materials” published before the vote, it described the framework as “a compromise to meet the unique circumstances of Northern Ireland” post-Brexit.

The EU has indicated that there can be no reset of the wider relations with the UK unless and until all elements on the Windsor framework, including permanent border control posts, are implemented.