Just days after the British Museum announced that it had fired an employee who was suspected of looting its storerooms and selling items on eBay, the museum’s director announced Friday that he was resigning, effective immediately.

Hartwig Fischer, a German art historian who had led the world renowned institution since 2016, said in a news release that he was leaving the post at a time “of the utmost seriousness.”

Mr. Fischer, 60, said that it was “evident” that under his leadership the museum did not adequately respond to warnings that a curator may be stealing items. “The responsibility for that failure must ultimately rest with the director,” Mr. Fischer said.

A few hours after Mr. Fischer’s resignation, the museum announced that its deputy director, Jonathan Williams, had also “agreed to voluntarily step back from his normal duties” until an investigation into the thefts was complete.

Trouble has been brewing at the British Museum since it announced last week that items had been stolen from its collection. The museum did not say how many objects were taken, or how valuable they were. But it said the missing, stolen or damaged pieces included “gold jewelry and “gems of semiprecious stones and glass” dating from as far back as the 15th century B.C.

Ever since, a stream of revelations around the museum’s handling of the thefts undermined Mr. Fischer’s position. On Tuesday, The New York Times and the BBC published emails showing that Mr. Fischer had downplayed concerns raised by Ittai Gradel, a Denmark-based antiquities dealer, about potential thefts.

In an email to a trustee in October 2022, Mr. Fischer said that “the case has been thoroughly investigated,” adding that “there is no evidence to substantiate the allegations.”

Mr. Fischer initially defended his response, saying in a statement on Wednesday that his handling of the allegations had been robust and that the museum had taken the warnings “incredibly seriously.” The extent of the problem only became clear later, he said, after the museum undertook “a full audit” of its collections.

His defense did little to quell criticism in Britain. On Wednesday, The Times of London wrote that the thefts were “a national disgrace, calling into question the museum’s own claims for its stewardship of cultural treasures, and for which it needs to give a full accounting.”

The unfolding drama was also watched closely in countries that seek the return of pieces in the British Museum’s vast collection, which includes more than eight million items, many from Britain’s former colonies. Lawmakers in Greece and Nigeria used the thefts as an opportunity to call for the return of contested artifacts.

Lina Mendoni, Greece’s culture minister, said in an interview on Monday with To Vima, a Greek newspaper, that the case reinforced her country’s demands for the return of the Parthenon Marbles, a series of sculptures and frieze panels, sometimes known as the Elgin Marbles, that once decorated the Parthenon in Athens. The thefts raised questions about the “safety and integrity of all of the museum’s exhibits,” Ms. Mendoni said.

And on Thursday, Nigerian officials reiterated their longstanding call for the British Museum to return a collection of artifacts known as the Benin Bronzes, which British troops looted in 1897.

Mr. Fischer’s time at the museum coincided with a sea change in attitudes over what rightfully belongs in the West’s museums, and an increase in the volume and intensity of restitution demands. He took over at the British Museum in 2016, having formerly run the State Art Collections of Dresden, a prestigious collection of museums in Germany.

In late July, shortly before the news broke that the museum had fired a worker suspected of theft, Mr. Fischer announced that he would step down next year. But as the crisis at the museum deepened this week, his position looked increasingly untenable.

The turmoil has come at “a very bad moment,” said Charles Saumarez Smith, a former director of the Royal Academy of Arts, in London. The British Museum is expected to announce a major renovation project that The Financial Times has reported will cost £1 billion, or about $1.26 billion, and the current uncertainty could make fund-raising much more difficult, he said.

The resignation was “an act of symbolic bloodletting,” Mr. Saumarez Smith said, but it may not end the British Museum’s woes. There are clearly “bigger issues that need to be resolved” at the institution, he added, including the questions about whether it has a handle on its inventory.

Mr. Fischer said in his statement that he expected the museum to “come through this moment and emerge stronger” but that he had “come to the conclusion that my presence is proving a distraction.”

“That is the last thing I would want,” he said.

George Osborne, the museum chair, said in the release that the board had accepted Mr. Fischer’s decision. “I am clear about this: We are going to fix what has gone wrong,” Mr. Osborne said. “The museum has a mission that lasts across generations. We will learn, restore confidence and deserve to be admired once again.”