They criticised around 10 directors who had worked up taxi bills of nearly €100,000 between them in 2013 and 2014, and also took aim at the "quite high level" of spending on business lunches.
Millepied -- husband of Hollywood actress Natalie Portman -- spectacularly quit the bastion of classical ballet in February after his plans to radically modernise its repertoire ran into the sand.
His arrival a little over a year earlier had been greeted with fanfare, with his supporters arguing that his stardust would revolutionise the world-renowned institution.
But the Cour des Comptes said in a report published Thursday that it could not see how a car and chauffeur for Millepied "could be justified" given no other manager enjoyed the same privilege.
The perk has since been abolished, and the Opera Ballet insisted Friday that its taxi bill for management and guest artists had been reduced by nearly a third since.
"The cost of work lunches also dropped by 10 percent last year," it added in a statement.
Auditors recognised that the company had "taken measures recently to bring spending in line with its financial restraints".
But it still called for an increase in the number of its productions which it insisted would help put the Opera Ballet on an even keel.
Insiders had criticised Millepied -- who came from a modern dance background -- for his programming which they said left many of the ballet's 154 classical dancers twiddling their toes.
"Too many new productions, notably lyric ones, do not have another run (40 percent) or only a single subsequent performance (26 percent)," the report said.
"Given the high cost of productions... the Opera cannot allow this to continue and must better manage its productions over time."