In a tale of murder leading to Burundi's elite, only Gustave the crocodile is clearly innocent

The plot is pure le Carré, but tailored for the tropics. A bloodied body washes up on a lake shore in a central African country. The nation is shocked when the victim turns out to be a top United Nations official, clubbed to a pulp and flung to the crocodiles.

Who could commit such a crime? Local police scramble into action, and make their arrests. But something smells rotten. A dogged reporter starts digging in the city's murky underworld. Soon a web of intrigue unfolds including rogue army officers, Western aid money and, maybe, the country's most powerful men.

It may read like fiction, but this is the real-life murder mystery gripping war-torn Burundi. Until 14 months ago Dr Kassi Manlan headed the Burundi office of the World Health Organisation (WHO). A sober public-health specialist from Ivory Coast in west Africa, he had the unglamorous but vital job of fighting disease in one of Africa's most bedevilled countries. But apparently he knew something important – something that made him worth killing.

One day in November 2001 Dr Manlan failed to arrive at work. Worried colleagues found blood stains on the floor of his suburban home. The next clue came that afternoon, by the lapping waters of Lake Tanganyika. The body was found by Didier, a middle-aged fisherman of tilapia who was casting below the colonial-era Cercle Nautique club.

In the Fifties and Sixties the Cercle Nautique was a place where Belgian colonials played pétanque and sipped red wine. Today that privilege is but a sepia memory. The yachts have sunk, the jetty is rotting and thirsty aid workers frequent the bar.

Standing on the rickety boards, Didier remembered the bloody corpse that slipped through the reeds on that November day.

"He was floating there," he said, pointing over the grey wash of the lake. Miraculously, the remains of Dr Manlan had not been touched by Gustave, the most elderly and notorious of the crocodiles of Bujumbura, the capital. Gustave is reputed to eat several city residents every year.

At first, it was hard to imagine why anyone would want to kill the doctor. Some whispered of a crime of passion, others of a professional grudge. A month later, the police produced their main suspect. They arrested Gertrude Nyamoya, a Burundian who had worked under Dr Manlan, and accused her of conspiring with a colleague, an epidemiologist, to kill their boss before he exposed a scam involving WHO money.

An open and shut case? Anything but. Four guards have since been charged with murdering Dr Manlan but two have said their confessions were extracted under torture. The epidemiologist fled the country under diplomatic immunity. And Ms Nyamoya, a WHO employee for more than 30 years, remains in jail. Her trial starts next month.

Many sceptics believe the 53-year-old divorcee is the patsy in a wider plot. Leading the charge is her brother, François Nyamoya, a lawyer who has gone to extraordinary lengths to prove her innocence. His cloak and dagger investigation could make a novel of its own. Over the past year he has paid informers and run secret surveillance. He traced phone records and vehicle licence plates. The trail led him, he says, to neighbouring Rwanda and a bank account in Paris.

The upshot, he says, is that a team of hired killers took Dr Manlan's life. Before murdering him, they forced the doctor to delete a file from his computer. Mr Nyamoya believes it contained information on stolen malaria drugs – possibly bought with European Union aid money. "That file must have contained the truth," he said, nursing a beer in a quiet corner of a Bujumbura bistro.

Alexis Sinduhije, one of Burundi's most fearless journalists, who has been running a parallel investigation, backs his claims. The murder appears to have been sanctioned by a powerful government figure and led by a serving army officer, he says.

"Burundi is such a small place that there is no way this could have happened otherwise," he says. The Burundi government dismisses such speculation as unfounded, and says the official inquiry is proceeding normally.

Whatever the truth, murder and intrigue lie at the heart of Burundi's problems. Nine years ago the country's first democratically elected president, Melchior Ndadaye, a Hutu, was assassinated by Tutsi paratroops. The ensuing war continues to this day – despite a faltering peace process – and Burundi society has become infused with secrecy, suspicion and corruption.

Will the full truth of Dr Manlan's death ever emerge? The self-appointed investigators are pessimistic. "This is a country," says Mr Sinduhije, "where the innocent pay the price for the acts of the guilty."