Marta Andreasen, who was sacked in May just four months into the job after criticizing EU accounting and financial reforms, said the problems had not been solved.
The commission, meanwhile, said that disciplinary procedures were under way against its former chief accountant and that she faced charges of breaching rules governing the conduct of employees.
"There are clear indications," said commission spokesman Eric Mamer in Brussels, that Andreasen "has violated" the rules.
Andreasen said there was a "dangerous failing at the heart of the (EU's) system" because of a "complete lack of compliance with basic and minimum accounting standards".
"The computer system on which financial transactions are processed is incoherent, insecure," she told BBC radio. "People can access this system" without being detected, she added.
Speaking late last week at a press conference in Britain's House of Commons, Andreasen said, "An institution that doesn't have an accounting system is open to big fraud."
She declined to estimate how much of the European Union's 98 billion euro budget was at risk, but said "taxpayers' money is at stake."
"I have been able to prove the systems are vulnerable but quantifying it is very difficult. I can no longer remain silent on the issues involved. They are critical to every member state and taxpayers, and represent a sad indictment of the failure within the commission to address concerns," she said.
"Not only has nothing been done to address well-known problems but there are attempts to silence those who do wish to address the issues constructively."
In Brussels, Mamer said that her criticism of the commission's accounting system "had already been made two years ago" both internally and by the European Court of Auditors.
Andreasen said her dismissal from her post "was decided behind my back and without any consultation. Since then, attempts have been made to prevent me from disclosing any information."
In a report supporting her criticisms, Britain's Financial Times said Aug. 1 that controls over the European Union's budget had been branded insecure and unreliable by the EU's court of auditors.
The system had "obvious risks as regards its reliability" stemming from a "lack of security," the report said, according to the FT.
The auditors' 1999 and 2000 reports criticised the commission's Sincom 2 accounting system, and the news paper suggested the problems persisted.
However, a source at the auditor's court told AFP that "new financial rules being applied as of Jan. 1 should make a big improvement."
One of the biggest problems is that in creating the system "no account has been taken of generally accepted accounting standards, mainly double-entry book-keeping," the new report said.