The commission, the EU's executive arm, is empowered to apply strict limits on public deficit and debt levels in the European Union, but the auditors said Brussels went to easy on offenders.
The commission "must be more strict," Milan Martin Cvikl, the member of the Court of Auditors responsible for the report, said in a press statement.
"It is not sufficiently aware of what is happening on the ground and it is not applying the rules consistently," he said.
The 120-page report said that even though "detailed procedures and guidelines" on budgetary discipline exist, "there are problems with the commission's implementation of these tasks.
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"This is because the Commission did not make full use of its powers to enforce" compliance by member states in applying the rules.
The report also cites a lack of resources and "poor record-keeping" from the commission's teams.
The report was based on studies of the work between 2009 and 2015 with six EU countries: Italy, France, Germany, Czech Republic, Cyprus and Malta.
But the countries, two of the most powerful members of the EU, have eluded punitive measures by the commission, which has drawn criticism that Brussels will not dare challenge governments on so sensitive an issue.
As an example, the auditors said last year's recommendation to grant France another reprieve "did not contain data in support of the baseline scenario ... Or any detail of additional discretionary revenue measures" France had promised in return for the delay.
At a news briefing, Commission spokeswoman Annika Breidthardt said the EU welcomed the court's work, "which can contribute positively to our own continuous effort to improve the functioning of the ... Process".