The 34-year-old officer was believed to have made off with the illegal drugs which have a street value of up to USD 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.
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.
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The missing cocaine has become a major embarrassment, with French media describing its disappearance as a real-life heist worthy of a crime movie.
On Thursday, 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 today is understood to have worked in the drugs squad for a number of years.