The European Parliament has overwhelmingly voted to ratify the UK-EU trade deal in an early morning vote in Brussels, as it branded Brexit a “historic mistake”.

MEPs backed the agreement by 660 votes in favour to five against, with 32 abstentions – representing the last political hurdle of the agreement.

The accord, which has been in provisional effect since 1 January, legally had to be approved before the end of April.

MEPs had been holding up ratification amid concerns that the UK was not implementing its side of the Brexit settlement with regards to Northern Ireland, repeatedly refusing to set a date for a vote.

Had the agreement not passed, the UK and EU’s terms of trade would have degraded even further – with tariffs and quotas applicable on goods.

But even with the free trade agreement in place, the UK enjoys far more limited access to EU markets than when it was a member state of the bloc.

In contrast to when Britain was in the single market, goods now have to be checked at borders and exporters now face significantly more bureacracy.

A resolution passed alongside the agreement by MEP said Britain’s exit from the EU was a “historic mistake” as no country could enjoy the same benefits outside the EU as inside.

Votes and debates are normally held at the European Parliament’s seat in Strasbourg, but the coronavirus pandemic means MEPs are using their alternative chamber in Brussels, or dialing in remotely.

Speaking after the vote, Boris Johnson claimed the deal’s approval was the “final step” in Brexit road, though in fact his government is still locked in negotiations over Northern Ireland.

Meanwhile European Commission president Ursula von der Leyen saidshe “warmly” welcomed the deal’s approval, adding: “The trade and cooperation agreement (TCA) marks the foundation of a strong and close partnership with the UK. Faithful implementation is essential.”

Lord Frost, the UK’s chief negotiator, thanked his EU counterpart Michel Barnier “for helping get us here”.

“Today’s vote brings certainty and allows us to focus on the future. There will be much for us and the EU to work on together through the new Partnership Council and we are committed to working to find solutions that work for both of us,” the minister said.

“We will always aim to act in that positive spirit but we will also always stand up for our interests when we must – as a sovereign country in full control of our own destiny.”

In a statement, Boris Johnson said: “This week is the final step in a long journey, providing stability to our new relationship with the EU as vital trading partners, close allies and sovereign equals.

“Now is the time to look forward to the future and to building a more Global Britain.”