The officers came from a special anti-crime squad and were being kept in custody, prosecutor Jacques Dallest said.
The 12 were arrested as part of an investigation into organised theft, extortion, violence and drugs, police spokesman Pascal Garibian said.
They are suspected of having stolen drugs and cash from dealers and taking cigarettes from illicit sellers.
"A few of them, apparently, were helping themselves and taking a cut," said Dallest, adding that the probe would gather more details of a practice that had been "spread across this service for a while."
Marseille prosecutors first opened a probe into the specialist squad at the start of the year after internal complaints.
In early September, a special committee on crime in Marseille, headed by Prime Minister Jean-Marc Ayrault, looked at crime in France's second-largest city.
The arrests are the latest in a series of incidents bringing French law enforcement under scrutiny.
In 2011, the deputy police chief of Lyon, Michel Neyret, was arrested after he was accused of accepting gifts and favours from members of the Lyon underworld.
He was charged in October 2011 with corruption, influence peddling, drug trafficking, and associating with criminals.
A former magistrate from Lyon, serving with prosecutors in Cayenne in French Guiana, was last month indicted for alleged corruption.
And in mid-September, seven Lyon police officers were accused of "passive corruption" where they allegedly traded favours with a drug-trafficking family.