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A convoy waits to enter a camp for the internally displaced in Maiduguri, Nigeria, Feb. 12, 2017. An estimated 4.7 million people in northeast Nigeria are desperately short of food and living in a region that is largely isolated from the world after years of brutal clashes between the Nigerian military and Boko Haram.ASHLEY GILBERTSON/The New York Times

The first surprise was the huge pile of cash: more than $43-million in U.S. dollars, stacked in hundreds of neatly wrapped bundles in the filing cabinets and wardrobes of an empty apartment in Nigeria's biggest city.

But the next surprise was even more shocking. After the money was discovered in a raid by Nigeria's anti-corruption agency, it was the national spy agency that claimed ownership of it. Many tenants of the upscale apartment building in Lagos, including the unit where the massive hoard of cash was found, were reported to be high-level officials and politicians.

The controversy escalated on Wednesday when President Muhammadu Buhari ordered a formal investigation and suspended the spy agency's director. And he added a new twist: He suspended another top civil servant in connection with a corruption probe into government relief funds for a humanitarian crisis in northeast Nigeria, where millions of people are facing a looming famine.

The two investigations are "related," Mr. Buhari's office said in a terse statement.

It was the latest evidence of the vast web of official corruption in Nigeria, where billions of dollars in oil revenue have been siphoned off by a politically connected elite in recent years, even as poverty and hunger have climbed to disastrous levels.

An estimated 4.7 million people in northeast Nigeria are desperately short of food and on the brink of famine. They live in a region that is largely isolated from the world after years of brutal clashes between the Nigerian military and Boko Haram, a radical Islamist militia. If some of their humanitarian funds have been stolen or diverted by government officials, it would mark a new low in the corruption that has haunted the country for decades.

Mr. Buhari was elected in 2015 on a promise to attack corruption and halt the Boko Haram insurgency in the northeast, but both of those crises have continued under his watch.

In recent weeks, the anti-corruption agency has found millions of dollars in U.S. and Nigerian currency in other locations around the country, including an international airport. The incidents were apparently unrelated, but gave a glimpse into the scale of illicit payments in the country.

In a separate case, news agencies reported that two international oil companies had paid $1.3-billion to the Nigerian government in 2011 in exchange for an offshore oil block, even though they knew that much of the money would be funnelled illicitly to a Nigerian politician. The companies have denied the allegation.

Mr. Buhari's statement on Wednesday gave few details of the alleged corruption, except that it involved the awarding of contracts under a Nigerian government program, the Presidential Initiative on the North East. It said the allegations of "violations of law" were focused on a senior official, secretary to the government, David Babachir Lawal, who is being suspended during the investigation.

Last year, Mr. Lawal faced allegations that he had awarded contracts to companies in which he had interests. He denied these.

It's not the first report of corruption in the region where millions are suffering from the Boko Haram conflict. In 2015, Mr. Buhari alleged that government officials had looted more than $2-billion in funds intended for weapons to fight Boko Haram, causing thousands of Nigerians to die needlessly. He said the money disappeared into "fictitious and phantom" military contracts, in which the ammunition and equipment was never provided.

More than 20,000 people have been killed in the Boko Haram conflict over the past eight years, and more than two million have been left homeless.

The second senior official to be suspended on Wednesday was Ayo Oke, director general of the National Intelligence Agency, one of the government's main security agencies, which has claimed ownership of the $43-million in cash from the Lagos apartment.

Mr. Buhari's statement said the investigation will inquire into "the circumstances in which the NIA came into possession of the funds" and "how and by whose or which authority the funds were made available to the NIA." The investigation will also find out whether the agency broke the law or security procedures by obtaining and using the cash.

In addition to the U.S. dollars, the anti-corruption agency found substantial amounts of British pounds and Nigerian naira in the Lagos apartment.

Mr. Buhari has ordered both of the investigations to report to him within 14 days.