Pascal Fauret, 55, and co-pilot Bruno Odos, 56, were arrested early Monday at their homes near the southeast city of Lyon.
They were both remanded in custody after appearing before French judges.
Both are awaiting transfer to the southern port city of Marseille, where the investigation is being conducted.
Fauret and Odos were arrested in March 2013 along with two other men as they were about to take off from the Dominican resort of Punta Cana.
Authorities said they were preparing to leave on a privately hired mid-size Dassault Falcon 50 jet with 26 suitcases containing 680 kilograms (1,500 pounds) of cocaine.
All four men deny they knew that the drugs were on board the plane.
The foreign ministry insisted the men had received no help from the French government.
Fauret's attorney Jean Reinhart confirmed that police arrived at his client's home at 7:00 am Monday with arrest warrants from the French judge who has been investigating the case, dubbed “Air Cocaine,” since February 2013.
Reinhart said the arrest warrant was “unnecessary”, adding: “It's all for show.”
Reinhart insisted his client and Odos had informed Christine Saunier-Ruellan, the judge in Marseille, that they would abide by any court summons they received.
“We were at the investigating judge's disposal,” said Pascal Fauret's wife, Sabine.
“Frankly, I had never imagined the police would show up at our doorstep,” she added.
The two other men convicted with them, Nicolas Pisapia and Alain Castany, remain in the Dominican Republic.
In August, all four were sentenced to 20-year prison terms but were not being held in detention pending a judicial appeal of their case.
However, they were barred from leaving the country.
It is still unclear how Fauret and Odos managed to slip out of the Dominican Republic a week ago.
The men reportedly travelled by boat to the Franco-Dutch island of Saint Martin before flying to Martinique and then on to France.
Eric Dupond-Moretti, Odos' high-profile lawyer, said at the time he could not give details of the men's journey because “it was not done alone, there were other people involved”.
But he said they had left of their own accord, telling reporters: “It's no use imagining that a team of spooks was paid by the French state to facilitate this escape. That's not it at all.”
France has suggested the pilots will not be extradited, though the Dominican Republic has issued an international arrest warrant for them.
Dupond-Moretti said he was “outraged and astounded” that the men had been arrested Monday. “We had asked that they summon us but it seems bad habits have prevailed,” he said.