The human rights chief at the European Union’s border agency said last week that it could suspend operations in Greece over chronic rights abuses against migrants, potentially pulling out dozens of border guards, vessels and aircraft from a key gateway into Europe.

The assessment, which was also made in an internal report obtained by The New York Times, came days after one of the decade’s most devastating migrant shipwrecks in the Mediterranean, a case that was not covered in the E.U. report because it was so recent.

That disaster has raised new questions about the conduct of the Greek authorities, including whether they did enough to help the boat while it was in distress.

The report by the E.U. official, Jonas Grimheden, adds even more pressure on Greece over its migrant policies. Mr. Grimheden cited the agency’s internal rules and several cases illustrating what he called the Greek authorities’ wrongful treatment of asylum seekers and migrants.

One case was the subject of a May investigation by The Times, which found that the Greek Coast Guard had rounded up and abandoned 12 asylum seekers, including women, children and a 6-month-old baby, on a raft in the Aegean Sea.

Mr. Grimheden told the agency’s board that his own investigation showed the findings were correct, and that the event violated E.U. and international law, according to a written summary by a European Parliament official present at the meeting.

In a confidential report to the border agency’s leadership, Mr. Grimheden advised the board on “possible steps to address the issue of the agency’s activities in Greece, in relation to Article 46,” which stipulates pulling out over fundamental rights violations.

But reflecting the complex reality of operating at one of Europe’s main gateways, he also recommended, in another section of the report, that the agency increase its presence and involvement in order to prevent further abuses.

According to the summary by the European Parliament representative, Mr. Grimheden urged “the strongest possible measures” to bring Greece “in line with national, E.U. and international law,” and he explicitly mentioned suspending operations in the country.

Mr. Grimheden’s recommendations are nonbinding and subject to the approval by E.U. governments and the European Commission.

The report, earlier reported by Le Monde, was delivered days after the shipwreck in the Mediterranean, on June 14. The disaster, which killed as many as 650 people, has left the E.U. agency, Frontex, and Greek officials debating where blame should fall.

The crew of a Frontex plane spotted the boat about 14 hours before it sank. The agency said in a statement that it shared images with the Greek authorities, alerting them to the boat’s precarious state.

The Greek Coast Guard has said that smugglers on the boat, which had departed Libya days earlier, refused assistance and that panic onboard caused it to capsize. Several survivors testified that it sank as the Coast Guard tried to tow it, a claim the Greek authorities have denied.

A Greek Coast Guard vessel, with the help of a superyacht in the area, rescued about 100 people, and as the accounts of survivors emerged, pressure mounted on politicians to find a culprit. Both Frontex and the Greek authorities have announced separate investigations.

Greek officials have consistently denied allegations of violating migrants’ rights, saying their migration policy is “tough but fair.”

Mr. Grimheden declined to comment about last week’s report, and Frontex said it could not comment on management board meetings because they are not public.

Frontex is tasked with a delicate mission: helping guard the European Union’s external borders while upholding the rights of newcomers, including to apply for asylum. It supports border countries like Greece by deploying guards from all over Europe and providing helicopters, boats, drones and other equipment.

Europe’s migration policy has significantly hardened in recent years, following the arrival of more than one million refugees, mostly from Syria, from 2015 to 2016. The migration fueled the campaigns of populist, far-right parties around the European Union, and contributed to a shift in mainstream E.U. politics to the right.

On Sunday Greeks re-elected the conservative New Democracy party, giving a vote of confidence to Prime Minister Kyriakos Mitsotakis, a leading proponent of a hard-line migration policy.

As the angst over migration has grown across the bloc, so has Frontex, which is now the bloc’s best-funded agency.

Frontex, too, has been accused of overlooking, covering up and even participating in human-rights violations. Last year, its executive director resigned over accusations of harassment, mismanagement and rights abuses, and the agency pledged reforms under new leadership.

But the alleged rights violations in Greece show the complexity of the task.

Mr. Grimheden has repeatedly recommended that Frontex suspend operations in Greece, saying in earlier reports that he had “credible reports” of the Greek authorities expelling migrants at land and sea, separating children from parents and treating migrants in a “degrading” way.

Instead of pausing operations, Frontex set up a joint “working group” with Greece.

Months later, Mr. Grimheden said in the latest report, “in substance nothing appears to have changed as regards the practices of the Greek authorities.”

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