"We are doing our damnedest to ensure there are accounting changes to address complaints about wrongdoing," he told the European parliament's budgetary control committee.
"Any evidence from staff is seriously treated, and there is career security for genuine whistleblowers."
Marta Andreasen was sacked as the EU's chief accountant in May after going public with claims that the EU accounting system was riddled with mistakes and loopholes.
Mr Kinnock said she had not followed correct procedures, and that her behaviour would not have been tolerated by any civil service in the democratic world.
Bad temper
In one bad-tempered exchange with the chairwoman of the committee, Dietmut Theato, who asked him to keep his answers short, he snapped: "I see, the commission is to be subjected to any attack. We are paid to be put in the stocks but we are never to respond?"
He insisted her complaints about flaws in the EU accounting system were known about before Ms Andreasen joined the commission and that she had been hired specifically to help put them right.
He also suggested that Ms Andreasen had been motivated by disagreements on policy, not because she had evidence of wrongdoing.
He added that the commission was in favour of "responsible whistleblowing" but not a "sneak's charter or an entertainment for the frivolous or malicious".
Complaints 'ignored'
Ms Andreasen is also expecting to be invited to speak to the parliament's budgetary control committee in the next two weeks.
She has said her complaints were ignored both by Mr Kinnock and Commission President Romano Prodi, and has accused Mr Kinnock of failing to clean up the Brussels bureaucracy.
Mr Kinnock acquired his role as EU sleaze supremo after complaints about corruption, cronyism and abuse of power led to the resignation of the entire European Commission in 1999.
The whistleblower on that occasion, Paul van Buitenen, finally left the commission last month saying that nothing had changed over the last three years.