There is widespread speculation in France that the prime minister might be forced to resign over his implication in a long-running legal case.
Mr de Villepin has been weakened by a row over labour law reform
A military official told magistrates Dominique De Villepin ordered him to probe corruption allegations against Interior Minister Nicolas Sarkozy.
The prime minister denies targeting his government rival, who has since been cleared in the case.
But the charge is a further blow after his failure to reform labour markets.
It is the first time Mr de Villepin has been linked to the legal case involving Clearstream, a Luxembourg-based financial institution.
Lists of beneficiaries of supposed illicit payments from Clearstream first emerged two years ago. They refer to bribes allegedly paid to French politicians over the sale of military frigates to Taiwan in 1991.
Among the names is that of Nicolas Sarkozy, the interior minister and Mr de Villepin's bitter rival ahead of presidential polls next year.
A French army general, formerly of the secret service, has told magistrates Mr de Villepin specifically asked him to investigate the inclusion of Mr Sarkozy in the Clearstream files, subsequently exposed as a forgery.
The prime minister, fighting for his political survival, is having to deny suggestions that he used state institutions to pursue a private vendetta.
Things could hardly have got any worse any quicker for Mr de Villepin, widely seen as the anointed successor to President Jacques Chirac.
Mr Sarkozy's popularity has a habit of growing in direct proportion to Mr de Villepin's failures. The latest of them, over attempts to make it easier to fire young employees, had already badly weakened the prime minister.
The French media suggests that legal troubles may yet follow political ones, should it emerge that Mr de Villepin did indeed try to discredit his rival.