BRUSSELS — Mounting evidence indicates that the European Union’s border agency has been complicit in Greece’s illegal practice of pushing back migrants to Turkey, according to documents obtained by The New York Times and interviews with officials.

In at least one case, Frontex, as the E.U. border agency is known, is accused of having helped cover up the violations, when a crew said it was discouraged by agency officials from reporting that they had seen the Greek authorities setting a boatload of migrants adrift in Turkish waters.

The case is currently being investigated by Frontex. But it has fueled suspicions that the agency, newly boosted in its role as upholder of the rule of law at E.U. borders, is not just sporadically aware of such abuses, but that it plays a role in concealing them.

“We are seeing an erosion of the rule of law at the E.U. borders which is willful,” said Gerald Knaus, a migration expert. “This is deeply worrying because it is eroding the refugee convention on the continent on which it was created.”

Throughout this year, The New York Times and others have reported on growing operations by the Greek Coast Guard to repel migrants from Greek waters back to Turkey, reports the Greek authorities deny amount to breaches of international laws.

But revelations that Frontex has witnessed pushbacks have thrown the agency into a governance crisis that threatens to further blight the European Union’s liberal values, once again calling into question the bloc’s commitment to upholding its own laws on refugees.

The cases have also highlighted a conundrum at the core of E.U. ambitions to tighten external borders by pooling resources and involving the bloc in the sensitive, zealously shielded work of sovereign border guards.

Frontex is the European Union’s best-funded agency, with a budget of over $500 million, and will soon deploy the first uniformed officers in the bloc’s history. It has been built up specifically to help in migrant-rescue operations as the burden of policing Europe’s borders has fallen most heavily on its peripheral states, like Greece.

It was also intended as a deterrent to the kind of mass arrival of refugees that sowed political crises across Europe after 2015, and fanned nationalist and populist movements.

Yet Frontex is not empowered to stop national border guards from committing violations, and it is not clear how it can play a role as standard-bearer of E.U. laws when informing on national forces risks the working relationships on which its operations depend.

Refugee arrivals to the European Union peaked five years ago and have dropped drastically since, but thousands of asylum seekers, many fleeing the wars in Afghanistan and Syria, still attempt the crossing. Unlike in the past, Greeks and their government have turned hostile to the new arrivals, exhausted by years in which asylum seekers have been bottled up in overrun camps on Greek islands.

There is also a growing belief in the Greek and several other European governments that aggression at the borders and poor conditions at migrant camps will make the attempt to reach Europe less attractive for asylum seekers.

Earlier this year, an analysis by The Times showed that the Greek government had secretly expelled more than 1,000 asylum seekers, often by sailing them to the edge of Greek territorial waters and abandoning them in flimsy inflatable life rafts in violation of international laws.

The Greek Coast Guard has rescued thousands of asylum seekers over the years but has become much more aggressive this year, especially as Turkey used migrants to provoke Greece by encouraging them to cross the border.

The Greek government has denied it is doing anything illegal in repelling migrant boats from its national waters, characterizing the operations as robust border guarding. But Mr. Knaus said “the denials are not serious,” and the practices are effectively happening in the open — under the eyes of E.U. border patrols.

The documents obtained by The Times describe, in Coast Guard vernacular littered with acronyms, codes, time-stamps and coordinates, a seemingly incessant Ping-Pong of migrant dinghies between Greek and Turkish waters, with Frontex crews on vessels or aircraft in observer status.

Four officials with direct knowledge of Frontex operations said that agency officials have been discouraging crews from filing reports on pushback incidents, and, in some cases, have stopped initial alerts of violations from being filed as “serious incident reports,” at times after consulting with the Greek authorities.

They all spoke on condition of anonymity because they were concerned about losing their jobs, or were not authorized to brief the press.

The Frontex spokesman, Chris Borowski, said the agency took the reporting of violations very seriously. “Pushbacks are illegal under international law,” Mr. Borowski said.

In the latest case to come to light, a Swedish Coast Guard crew on deployment under Frontex witnessed a pushback to Turkish waters of a boat full of migrants by the Greek authorities on Oct. 30 off the Greek island of Chios.

The Swedish crew was later advised by a Frontex officer to not report it, documents reviewed by The Times show. The Swedish representative to the management board of Frontex described the incident, and the suppression of the attempt to report it, at a meeting on Nov. 10 — the first known case of an E.U. member state reporting active interference by Frontex officials.

The Swedish government did not comment. A spokesman for Frontex said the agency wouldn’t comment because of an “ongoing procedure.”

Frontex has been working in Greece for more than a decade, providing sea, land and aerial surveillance and rescue capabilities and deploying crews from other member states under its command.

The details now emerging push the agency deeper into a governance crisis which began in October when a consortium of news organizations, including the German newsmagazine Der Spiegel, reported a number of occasions when Frontex crews witnessed pushbacks in Greece.

The European Commission, which is part of the Frontex oversight system but does not control the agency, pushed for a special inquiry into these allegations and, at an emergency agency board meeting on Nov. 10, asked its leadership to answer detailed questions in writing.

The answers arrived with a four-day delay, just 15 hours before the start of another meeting to discuss the problems on Wednesday. Yet another emergency meeting has been called in December, mounting pressure on the agency.

Frontex has promised internal investigations but also quickly dismissed allegations, saying for example, in a letter seen by The Times, that it would look into the Swedish case, but that it had so far found no evidence that it happened.

How these investigations shake out will matter a great deal for the future of Frontex, which was once little more than a back-office operation in Warsaw but now finds itself on the front lines of the nettlesome issue of migration that has the potency to make or break governments.

Apart from helping member states with asylum-seeker arrivals, Frontex’s role as an E.U. agency by law is to respect fundamental rights, and bring up human-rights standards across national E.U. border agencies, which often don’t have a strong culture of upholding them.

But claims that Frontex does not take fundamental rights seriously enough are growing. This year, only one million euros in its budget of 460 million euros — about $548 million — was allocated to rights monitoring.

The agency was supposed to hire 40 fundamental-rights officers by Dec. 5 but the jobs have not yet been advertised. The agency is currently hiring for their boss, after years of staffing issues around that position. A Frontex spokesman said the delays stemmed from the coronavirus pandemic.

Documents seen by The Times laid out how in one episode the Greek authorities were consulted before a report was made, and were able to suppress it. On Aug. 10, a German crew deployed by Frontex reported that a Greek Coast Guard vessel “took up border control measures prohibiting the landing to Samos.”

The expression refers to maneuvering and making waves around a dinghy to repel it. The event was not recorded as a “serious incident,” because, the document said, the Greek Coast Guard argued the activities “do not provide any ground” to initiate such a report.

Another incident, which a Frontex aerial crew observed and reported in detail to its headquarters, took place on the evening of April 18 to 19 off the coast of Lesbos, and lasted more than five hours.

A dinghy was detected by the Greek authorities and approximately 20 migrants were rescued and put on board a Greek Coast Guard vessel shortly after midnight, their empty dinghy towed by the Coast Guard toward the island.

But instead of being taken to shore, at 2:45 a.m., the migrants were put back on their dinghy and tugged to Turkish waters by the Greek Coast Guard, the Frontex aerial crew reported.

As events unfolded, the Greek command center twice asked the Frontex aircraft to change its flight path, directing it away from the incident.

“At 03:21 Frontex Surveillance Aircraft communicates that the rubber boat has no engine and it is adrift. Greek assets are departing the area leaving the rubber boat adrift,” the document said.

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