The 34-year-old officer was believed to have made off with the illegal drugs – which have a street value of up to two million euros (Sh235mn) – after security cameras spotted a person resembling him entering the headquarters with two bags, according to a statement from police and prosecutors.
The officer, who works with the Paris drugs squad, was arrested near Perpignan close to the Spanish border where he was on holiday.
He is being questioned by officers in the region before being transferred to Paris.
Interior Minister Bernard Cazeneuve has called the allegations “extremely serious”, and said that the man had been suspended pending an investigation.
“If the investigation confirms his involvement, and as soon as I have any news on the conclusions of the inquiry, I will not hesitate in taking all the necessary measures,” he said, without elaborating.
The missing cocaine has become a major embarrassment, with French media describing its disappearance as a real-life heist worthy of a crime movie.
Police sources said several searches were currently taking place, both in Perpignan and at the officer’s Paris home.
Colleagues expressed surprise at the arrest, describing the suspect as “unassuming” and “trustworthy”.
The drug cache was seized in a Paris raid in early July which led to several arrests.
On Thursday, police learnt the drugs had gone missing from a secure room in the police headquarters, which overlooks the Seine river close to the famed Notre Dame cathedral.
The haul had been kept in a high-security area, with security procedures requiring anyone entering the room to sign-in and be accompanied by another officer authorised to have a key.
A number of elite police officers were grilled on Friday by a team from the national police’s internal affairs division over the incident.
The headquarters attracted unwelcome attention in April when two elite French officers were charged with raping a Canadian tourist there in a case that sent shockwaves across France.