BRUSSELS — The European Parliament has voted by a large margin to give the European Union’s final approval to a Brexit deal already beset by difficulties, complaints and a court challenge.
The tally, released Wednesday, was 660 in favor, with five against and 32 abstentions.
While the outcome was never really in doubt, the Parliament expressed considerable concerns about the trustworthiness of the current British government to carry out its side of the Brexit bargain, including the trade deal that was just approved.
That agreement, which governs trade and customs issues and provides for zero tariffs and zero quotas, has been applied conditionally since the beginning of the year. But a negative vote by the European Parliament would have killed it, producing the “no-deal Brexit” that neither side favored.
The deal leaves out key issues like financial services and foreign and security policy. Debates and consultations over how best to implement the trade deal and the general withdrawal agreement in real life seem fated to extend indefinitely.
The vote marks the end of a long, winding and often bitter road that many have compared to an angry divorce after nearly 45 years of marriage. Britons voted to leave the European Union after a campaign filled with exaggerations on both sides nearly five years ago, in June 2016.
Britain is now on its third prime minister since then. The struggle over how to define Brexit and Britain’s future relationship with the European Union destroyed the prime ministerships of David Cameron, who was sure that Britons would choose to remain, and of his successor, Theresa May, who failed to sell a Brexit that would keep Britain closer to Brussels.
Boris Johnson wanted a more defined break, giving Britain the power to set its own regulations and standards, which entailed pulling the country out of Europe’s single market. But that raised the thorny issue of the border between Northern Ireland, which is part of Britain, and the Republic of Ireland, which is a member of the European Union.
All agreed that to keep the peace on the island of Ireland, there could not be the restoration of a land border. To solve the problem, Mr. Johnson proposed a border in the Irish Sea, which came into force with the Withdrawal Agreement. It has since become the source of considerable problems and aggravations with new customs duties and health checks, and Brussels accuses Mr. Johnson of scheming to eliminate them.
The European Parliament had delayed its vote to protest Britain’s handling of Northern Ireland and the protocol. Britain’s actions are the source of a legal complaint filed by the European Commission, the bloc’s executive, after Britain unilaterally extended grace periods for not conducting checks on goods being transported between Northern Ireland and the rest of Britain.
That mistrust ran through the debate over the trade deal, called the Trade and Cooperation Agreement. Christophe Hansen, a key legislator on Brexit from Luxembourg, said that a positive vote “should not be seen as a blank check to the U.K. government or a blind vote of confidence in that they will implement the agreements between us in good faith, but it is rather an insurance policy from our perspective.”
The agreement, Mr. Hansen said, “will help us remind the United Kingdom of the commitments it has signed up to.”
Manfred Weber, a German who heads the largest party grouping, the center-right European People’s Party, put it bluntly on Twitter. “We will vote in favor of the post-Brexit T.C.A.,” he wrote, referring to the trade agreement. “But we are concerned about its implementation, because we do not trust Boris Johnson’s government.”
There were also numerous worries expressed about Britain’s misusing or undermining the complicated arrangements on fishing rights.
David McAllister, a German legislator who is half Scottish, dismissed some of the problems as teething issues. But he said that some derived from “the kind of Brexit the U.K. has chosen for itself,” which will mean increasing divergence from the European Union single market. That by itself will require continuing discussion, he said, as well as working through areas left out of the Brexit deal, including financial services and foreign and security policies.
Brussels is committed to work on practical solutions between Northern Ireland, mainland Britain and Ireland, he said. “But the protocol is not the problem, it is the solution. The name of the problem is Brexit.”
Asking Parliament to ratify the deal, the Commission’s president, Ursula von der Leyen, promised that Brussels would use the dispute and enforcement mechanisms in the deal to ensure compliance by Britain. If not, she said, she would not hesitate to impose punitive tariffs.
“The agreement comes with real teeth — with a binding dispute settlement mechanism and the possibility for unilateral remedial measures where necessary,” she said. “We do not want to have to use these tools. But we will not hesitate to use them if necessary.”
Unhappy with Britain, the Parliament had delayed ratification twice. But the conditional implementation would have run out at the end of April, so the Parliament finally cast its vote.
After a debate of nearly five hours on Tuesday, the legislators, many of whom were attending virtually, voted remotely, with the final totals revealed on Wednesday morning.
Michel Barnier, who was the E.U.’s chief negotiator with Britain, thanked the legislators for their diligence. He praised the deal but warned: “Everyone has to shoulder responsibility and respect what they have signed up to.”
He summarized the feelings of many when he said: “This is a divorce, a warning and a failure, a failure of the European Union, and we have to learn lessons from it.”
Responding to the vote, Mr. Johnson said in a statement that “this week is the final step in a long journey, providing stability to our new relationship with the E.U. as vital trading partners, close allies and sovereign equals.”
Ms. von der Leyen has said that ratification would mark a new chapter in relations with Britain, for good or bad. She hoped, she said, that it would represent “the foundation of a strong and close partnership based on our shared interests and values.”
The complications of Brexit, and the continuing struggles over its implementation, have served if nothing else to end talk in the rest of the European Union about making a similar exit.
Monika Pronczuk contributed reporting.