The head of Nigeria’s national intelligence agency has been suspended after $43m (£34m) in cash was found in an empty flat in the capital Lagos.

The country’s president, Muhammadu Buhari, has ordered an inquiry after the dollar haul, along with £27,800 and 23.2m naira (£94,000), was discovered by anti-corruption investigators.

The economic and financial crimes commission (EFCC) said it seized the “humongous” amount of money in an apartment in Ikoyi, an upmarket area of the city.

Ayo Oke, director-general of the NIA, has been suspended during a two-week investigation into how the agency acquired the money and whether it did so legally.

The cash, in sealed plastic wrappers, was hidden in filing cabinets and behind hidden panels in a wardrobe.

It was discovered by EFCC officials after a tip-off that a woman involved in “suspicious movement of bags in and out of a particular apartment in the building”.

“She comes looking haggard, with dirty clothes, but her skin didn’t quite match her appearance, perhaps a disguise,” said the EFCC statement, quoting an anonymous source.

In a separate development, Mr Buhari, who took office in May 2015 promising to crack down on corruption, also suspended a senior civil servant over the use of funds intended for handling a humanitarian crisis in the northeast of the country.

An investigation has been launched into contracts awarded under the presidential initiative on the north east, where 4.7 million people, many of them refugees from the Boko Haram Islamist insurgency, are in dire need of food.

A three-man committee headed by vice-president Yemi Osinbajo is to conduct both investigations.

Last week, the EFCC lost a key battle as a Lagos court lifted an order freezing $5m (£6.4m) in a bank account operated by Nigeria’s former first lady Patience Jonathan, prompting ministers to insist the anti-corruption campaign was on track.

But the main opposition party has accused Mr Buhari of conducting a political witch-hunt because many of those arrested and charged in the war on corruption are opposition party members or served in the previous administration.