In 2013 and 2014, about 10 senior figures spent close to €100,000 (£85,000; $112,000) per year on taxis alone, it says.
New managers at the Opera say they are cutting costs.
But the criticism comes amid wider claims of abuse of expenses in the Paris art world.
With its gilded gods and crystal chandeliers, the Paris Opera takes spectators back to a time of opulence and the pleasures of high society.
But its image of extravagant aristocracy chimes awkwardly with the French government's struggle to reduce the public deficit. The audit report's revelations have been called "tragic" and "embarrassing" by the French press.
The report also criticises choreographer Benjamin Millepied for having a car and a chauffeur, an expense the auditors deemed "not justified". Mr Millepied, who is married to Hollywood actor Nathalie Portman, has since left the organisation.
Paris Opera did not respond to requests for an interview. In an interview with Le Parisien, deputy director Jean-Philippe Thiellay, who arrived in August 2014, stopped short of criticising his predecessors but insisted the new management had "drawn the right conclusions and turned the screw" on improper practices.
Paris Opera also said it had cut taxi expenses by 30% and restaurant bills by 10% in 2015.
But even the new management - under Mr Thiellay and director Stephane Lissner - were reprimanded for spending €59,900 on the lavish renovation of four offices.
The work included a new carpet, paintwork and furniture, according to the audit.
"We moved a partition wall and I don't think it's wrong to want to change the carpet," Mr Thiellay told Le Parisien.
The kerfuffle over expenses at the Paris Opera - which runs two venues, Opera Garnier and Opera Bastille - comes after several other expenses scandals in the French capital:
The report said the financial situation of the Opera was "quite fragile" despite receiving €96,751,005 in public subsidies this year, over half of the Opera's total budget.
France's audit body, the Cour des Comptes, has accused Paris Opera directors of misusing public funds on taxis, restaurants and food.