But her resignation comes after the authorities opened an inquiry in March into the central bank’s operations. The government in December spent $5.6 billion on a recapitalization of PrivatBank, which is owned by Ihor V. Kolomoisky — the pro-Kiev commander of a battle-hardened militia and the governor of a crucial region that is on the front line of the Russian conflict.
Ms. Gontareva, who took the post in 2014, closed half of Ukraine’s private banks. That was part of efforts to carry out a “total revamp of the Ukrainian banking system,” she said in a recent interview.
Not everyone was pleased with her efforts. At one point during her tenure, she found a coffin dumped outside her home.
Among the moves she oversaw were deals offering PrivatBank central bank refinancing to strengthen the lender’s balance sheet. But at least $1.8 billion of that money quickly vanished into bad loans, according to the Anti-Corruption Action Center, an independent organization tracking fraud in Ukraine that is financed in part by United States government grants. By December, PrivatBank faced a huge capital shortfall.
“When I opened their books as governor of the central bank, I was shocked,” Ms. Gontareva said. “Instead of real assets, they have just shells.”
PrivatBank, with nearly a third of Ukraine’s individual bank deposits, was too big to fail, particularly in a country destabilized by war. The government in Kiev soon stepped in with the $5.6 billion bailout, nationalizing the lender.
Through it all, Mr. Kolomoisky was financing a major anti-Russian militia in the war in eastern Ukraine. The militia, called Dnepro-1, remains well regarded by Ukrainian soldiers and was crucial in holding parts of the front line before the regular army could be transformed into a battle-ready state.
That support for the militia insulated his business activity from aggressive oversight by the government he was defending militarily, said Tymofiy Mylovanov, president of the Kiev School of Economics. “People respect him for helping to save Ukraine,” Mr. Mylovanov said.
But the collapse and rescue of PrivatBank have raised questions over whether Ukraine can adequately manage its economy and safeguard the funds from its $17.5 billion I.M.F. program, as well as billions more in bilateral lending. The PrivatBank bailout alone cost Ukraine the equivalent of 5 percent of its gross domestic product, according to Standard & Poor’s, the rating agency.
While the I.M.F. and other lenders attached conditions to that money, they were largely tied to economic and political reforms. Of the about $8.3 billion that has so far been disbursed, $2.7 billion was handed to the government for budget support and the remainder transferred to the central bank to bolster currency reserves. The bailout of PrivatBank has cost the government more than the entire I.M.F. budget aid received since the 2014 revolution.
Instead, the I.M.F. mandated the creation of an independent anticorruption watchdog. On March 29, agents from that body searched the central bank’s headquarters as part of a half dozen criminal inquiries into “misuses or misappropriation,” of central bank funds, including one looking specifically at possible wrongdoing by central bank employees, according to a spokeswoman.
Independent anticorruption groups say the March raid was related to accusations of impropriety over refinancing deals with failing, oligarch-controlled lenders, like PrivatBank.
Ms. Gontareva has protested her innocence and said bank closings during her tenure had in fact put an end to refinancing fraud in Ukraine. She said that the central bank had forwarded recommendations for criminal prosecutions for loan fraud to the authorities but that with the judicial system still largely unreformed, few cases had made it to court.
“Sad to say, some of these loans were extended with the full knowledge that they would never be paid back,” said Frank Gill, an analyst with Standard & Poor’s. “That is how things worked in the past, and Governor Gontareva had the unenviable task of cleaning that up.”
The former central bank chief blamed criticism of her work in the Ukrainian media, and the death threats, on disgruntled businessmen unhappy with her efforts to close banks. She described the corruption investigation as “nothing special” and said it was one of several audits and reviews of the central bank.
She said she had carried out tough reforms, reducing the bloated size of the central bank’s staff, which at one point numbered 12,000; slashed inflation to single digits from 43 percent in 2015; and moved the country to a more flexible foreign exchange system.
Ms. Gontareva said she was planning to take some time off and re-enter the private sector — she previously worked for a brokerage firm in Ukraine — adding that she hoped never to be a bureaucrat again.
A former spokesman for Mr. Kolomoisky, Borys Braginsky, said in a telephone interview that he had no means of contacting the businessman. He added that Mr. Kolomoisky had not retained a new spokesman and could not be reached for comment.
With so much money at stake, political pressure is mounting on the Ukrainian anticorruption watchdog, which is investigating the central bank and which last summer revealed secret payments in Ukraine to President Trump’s then campaign manager, Paul J. Manafort. Rival factions in Parliament have clashed over the appointment of an outside auditor to the organization.
The I.M.F. has now tightened its conditions for lending.
In February, it listed the creation of an anticorruption court, free from political interference, as a benchmark for future disbursements. It said in written replies to questions that it was considering elevating some requirements from benchmarks to “prior action” demands, or conditions that a country must meet before the fund’s board will even convene to consider releasing a new tranche of funding.
There is little dispute that the central bank had to close several shaky banks in Ukraine, said Daria M. Kaleniuk, the executive director of the Anti-Corruption Action Center. But the hefty cost to Ukrainian taxpayers and Western donors, including the United States, was most likely too high because the failing banks — most disastrously PrivatBank — were refinanced shortly before they collapsed.
The eventual loss from PrivatBank, Ms. Kaleniuk said, should have been obvious to the central bank before it cost donors and taxpayers billions.
“This scheme could have been noticed by the central bank and by Gontareva,” Ms. Kaleniuk said. “The problem is, nobody has been punished yet for such a huge fraud.”