The word most often used to describe the imposing 36 Quai des Orfèvres – France's equivalent to Scotland Yard – is mythique, or legendary. Home to the Police Judiciare, nicknamed les flics, the building flanking the river Seine at the heart of Paris has been the backdrop for films, novels and television series broadcast around the world.

Commissioner Maigret, the celebrated pipe-smoking detective created by Georges Simenon, roamed its labyrinthine "damp, cold and airless" corridors, as did actors Gérard Depardieu and Daniel Auteuil in the film named after the building. British viewers will be more familiar with the name through the travails of Captain Laure Berthaud in the French series Spiral (Engrenages) on BBC4.

These fictional fighters of crime and corruption, however, might have struggled to solve what might be titled The Mystery of the Missing Cocaine, which is making 36 Quai des Orfèvres look more lackadaisical than legendary.

A week after an officer from the drugs squad – known as les stups – was arrested and accused of strolling into the police headquarters one evening and coolly strolling out again with 52.6kg of cocaine in two holdalls, fact is proving stranger and more impenetrable than fiction.

Investigators are puzzled how a thief could have removed the drugs, packaged in 48 foil wrapped "bricks" and with a street value of more than €2m, from a triple-locked high-security room to which only three senior officers supposedly had the key. And they are perplexed why one of their own, who knew the building, the procedures and the position of CCTV cameras, would apparently do so.

"Incredulous is the word," one officer said.

The cocaine had been seized on 4 July in the 18th arrondissement of Paris during a raid on a drug-dealing network. A few days later, the bricks were sealed, labelled and locked in the high-security seized evidence room by one of the three senior officers – the police chief of staff, his deputy and the head of the drug brigade – who have access.

The rules are strictly applied: officers who wish to enter the so-called "yellow room" have to sign a request stating the object of their visit and be accompanied by a key holder.

On 31 July, the cocaine was missing. The door and lock of the yellow room were intact.

The Interior ministry's police investigations team, the IGPN, known as the "police's police", were summoned and found CCTV footage of an officer arriving at 36 Quai des Orfèves late on 24 July with two apparently empty bags and leaving shortly afterwards with two bulging bags. A female officer in the guardroom reported seeing the officer, and colleagues identified him from the video.

Records allegedly show he made what an investigator described as a "feeble excuse" to visit the sealed room shortly before the drugs disappeared.

On Saturday, Jonathan Guyot, a 33-year-old drug squad officer, was arrested while shopping in the southern French city of Perpignan, where he was born, with his wife and 11-month-old daughter. In his backpack, the arresting officers allegedly found €16,020 in cash. A further €8,790 in cash was found at his Paris home. They were large sums for a policeman earning at most €2,000 a month. He was found to own two properties in Perpignon and five small studio flats in Paris.

Guyot's arrest stupefied colleagues. He was described as beau gosse (handsome), sporty, hardworking but discreet, and a model police officer with a good record.

After four days of questioning, he was brought before a judge and put under formal investigation, the equivalent of being charged, over the theft of the cocaine. No trace of the drugs has been found.

Guyot has denied the charge and said he won the cash found in his rucksack gambling online, a claim confirmed by his younger brother Jérémy, who was with Guyot shortly before his arrest.

"He was calm and was on holiday. He said they wouldn't find anything against him," Jérémy said. "It's ridiculous that he would steal that from 36 [Quai des Orfèvres] … he's not a big spender, he doesn't particularly need money, and the money he earns honestly."

Investigators are now looking for possible accomplices. A second drug squad officer, aged 30, was arrested and released on the equivalent of police bail, and a member of the French border police, who allegedly had been in contact with Guyot, presented himself for questioning.

In an unexpected twist, sniffer dogs brought in to check a garage allegedly linked to the suspect found no trace of cocaine – but uncovered 200kg of cannabis resin in a neighbouring lockup.

A French crime reporter working on the story told the Guardian the theft had echoes of the spectacular heist carried out by Toni Musulin, a Frenchman of Serbo-Croat origins who in November 2009 stole €11.6m from an armoured security van he was driving. Police later found €9.1m behind a false wall of a garage. Musulin, who turned himself in, admitted stealing the money, and was convicted and jailed. He was released in September last year, but €2.5m of the stolen money has never been found.

"It's all very strange. Whatever the reputation of 36 Quai des Orfèvres, things don't just disappear like that," said the journalist, who did not want to be named.

"There are three sorts of evidence that are a real headache to deal with – money, drugs and weapons – and they are put under seal and closely guarded. But if the drugs are not found, if there are no suspicious movements of money and all the police have for evidence is the silhouette of someone on a CCTV camera, that's not going to get a conviction.

"I have no idea how this story is going to finish. I'm not sure the police have either."