Nikki Sinclaire, who represented the West Midlands region in Brussels and Strasbourg until 2014, signed and submitted "significant" expenses "in excess of the flight costs", according to the prosecution.
On Wednesday, it emerged in court Sinclaire had gone to the European Parliament's MEPs' expenses chief to raise concerns about irregularities in her own claims.
Francisco Estela Burriel told Birmingham Crown Court that Sinclaire "told me that she is not sure, but probably the (expenses claims) declaration has been made by another person, a member of her staff".
Her barrister Sean Hammond asked if he recalled the meeting in Mr Estela Burriel's office, from late August 2010, over a year before her arrest by West Midlands Police in February 2012.
Addressing the EU mandarin, he said: "The concern she raised was she believed because of a document she had seen in her office in Birmingham, that a member of staff had deliberately corrupted expenses claims submitted to your office."
The 56-year-old bureaucrat replied: "Yes, absolutely."
He advised Sinclaire to contact the travel companies involved to trace the paperwork, but she later told him she was "unable to find the flights she flew and which company she took to travel" as she tried to trace and correct the errors.
Earlier, Sinclaire's barrister had asked whether newly elected MEPs' staff received any formal training on expenses.
The EU civil servant replied that there had been a three-week information drive at the European Parliament, and that all the information was "made public".
Sinclaire's lawyers have claimed that the amount actually overpaid was about 3,000 euro (£2,465), but deny any wrong-doing on her part.
But the Crown has alleged Sinclaire deliberately submitted 10 travel expense claims for road travel, which she actually undertook more cheaply by flying from Birmingham Airport to the heart of EU government.
Antonie Muller, opening the prosecution case on Monday, told jurors it was a quirk of the Brussels expenses system that an elected member could claim for their journey time "duration", which would be longer for road trips than for a flight.
In six out of the 10 claims, the Crown has alleged that is what Sinclaire did, including one occasion where she claimed to have driven to Stoke-on-Trent when in fact she was in Cyprus.
In his evidence, Mr Estela Burriel revealed some of the inner workings of the MEPs' expenses bureaucracy, including the fact elected members can claim for up to 800 kilometres (497 miles) of road travel within their home country without submitting receipts.
As he left the court, the Spaniard covered his face with his bag after spotting media photographers outside.
Opening the case on Monday, Mr Muller said: "In short this is a case about a member of the European Parliament thereafter, an elected official making false and dishonest claims for travel expenses during her office."
Sinclaire, 47, of Shirley, Solihull, West Midlands, is accused of misconduct in a public office between October 1 2009 and July 31 2010 while a serving member of the European Parliament by making or causing to be made false or dishonest claims for travel expenses.
She is further charged between October 14 2009 and December 31 2010 of fraudulently transferring criminal property into her bank account.
At the start of the trial Judge Stephen Eyre QC told the jury: "This is not a trial about politics, but about particular events in a particular time and about the intention of which certain things were done.
"Whether you agree or disagree with the defendant's politics is irrelevant to this trial."
Sinclaire, on bail, denies all the charges and the trial continues.