The 34-year-old officer was believed to have made off with the illegal drugs — which have a street value of up to €2 million ($2.7 million) — 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.
Searches are currently taking place both in Perpignan and at the officer's Paris home, according to a police source, and it is understood he will be flown to Paris for questioning.
Interior Minister Bernard Cazeneuve has called the allegations "extremely serious", and said that the officer — who has not yet been named — had been temporarily suspended.
"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," Cazeneuve 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.
The drug cache was seized in a Paris raid in early July and was being kept in a secure room in the police headquarters, which overlook the Seine river close to the landmark Notre Dame cathedral.
, police learnt the drugs had gone missing.
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 have been grilled by a team from the national police's internal affairs division over the incident.
The officer arrested on Saturday is understood to have worked in the drugs squad for a number of years.
Colleagues described the suspect as "unassuming" and "trustworthy", with one source saying he had been in telephone contact with his unit to discuss active cases earlier Saturday.
The headquarters at Quai des Orfevres 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.
The 34-year-old woman said she was raped in the building after meeting the officers during a night of heavy drinking at an Irish pub.