The Clearstream affair was one of France's largest political dramas in 2006, involving allegations of tax evasion and money laundering.
The scandal goes back to 2003 following questions over France's sale of six frigates to Taiwan.
Accusations were made that the deal allowed a number of politicians to receive percentage fees as a result of secret Clearstream accounts.
"People manipulated this affair"
political adviser to Sarkozy
A list of the secret accounts, including one with Sarkozy's name, was proved to be false, but investigations continued in what Sarkozy said was an elaborate attempt to discredit him.
Clearstream is the electronic clearing unit of Deutsche Boerse AG, based in Luxembourg.
Francois Fillon, Sarkozy's political adviser, said although he had no proof, he believed "people manipulated this affair".
The affair destroyed relations between Sarkozy and De Villepin and has affected next year's race for the French presidency.
Sarkozy, seen by many as a victim, has emerged from the affair as a favourite to win the presidential nomination for the centre-right UMP party.
But suspicions that De Villepin was involved, combined with his shelving of proposed labour reforms earlier in the year provoking violent protests across the country, have left him unlikely to run for president.
He has not ruled out a presidential bid, but has said he has no "presidential ambitions".
Sarkozy's supporters have called for punishment if the investigation establishes that the apparent smear campaign was aimed at unsettling the minister's presidential bid.
|Nicolas Sarkozy is seen by many as|
a victim of the scandal [EPA]
Fillon said: "When low blows are used to sideline a political adversary, there must be sanctions."
Michele Alliot-Marie, France's defence minister and another potential presidential rival for Sarkozy, was questioned over the Clearstream affair in November.
Thursday's questioning is only the second time that a judge has questioned a French prime minister as a witness.
Lionel Jospin, a former socialist prime minister, was questioned over party financing in 2001.