Pieper, speaking at a press conference on Thursday ahead of parliament's plenary vote in Brussels on the 2012 discharge, said that 95 per cent of EU expenditure was "carried out in an orderly fashion".
However, the German MEP, who is rapporteur for the budget discharge on the European commission and executive agencies, stressed that the majority of the remaining five per cent of spending that did not meet the required standards occurred in eight member states that had been "previously flagged up", suggesting that the cause was "a structural problem that needs to be improved".
He highlighted "regional and agriculture" spending as two areas of particular concern, but added that the European commission is "committed to bringing in proactive controls" in these areas.
"We need more direct controls on the beneficiaries of funding and not just leave it up to member state auditors" - Markus Pieper
Pieper's report calls for a "parliamentary reserve on agriculture and cohesion", allowing parliament to issue a reservation on areas of spending where it feels it has not received "adequate assurance" from the commission or court of auditors to allay its concerns.
His report regards reserves as a "new and effective budgetary control instrument, being a commitment by parliament to monitor closely the measures taken by the commission and member states" to eliminate problems related to EU spending.
The EPP deputy said that he failed to understand why parliament's S&D and Greens/EFA groups wanted to "delete reservations" from the report, adding that he felt the introduction of this procedure could bring "a more strategic approach to this financing period".
"We need more direct controls on the beneficiaries of funding and not just leave it up to member state auditors."
He also voiced his criticism of an alteration made to the discharge report by parliament president Martin Schulz, calling the move a "curious procedure" that "sets a bad precedent".
Schulz has come in for criticism for his removal of a paragraph which was critical of him for delaying the work of the budgetary control committee, with EPP deputy Inge Gräßle calling it "a real scandal".
The paragraph concerned Schulz's withholding of a Belgian court invitation to MEPs and the postponement of committee hearings, with both instances related to the case of Maltese former health commissioner John Dalli.
Schulz's spokesperson Armin Machmer said the alteration to the discharge was "totally standard procedure" as the piece of text was in "contradiction with legal obligations binding the institution… with regard to confidentiality rules".
Petri Sarvamaa, who headed up several discharge reports on individual EU agencies, highlighted the "political importance of creating trustworthiness" by showing European citizens that the people working in decentralised agencies "are trying to do a good job".
"We will send a strong message to every agency that they must do the best they can to properly use the money of taxpayers" - Petri Sarvamaa
"This is not always mentioned in European parliament and the discharge process," he added.
The Finnish deputy stressed that the euro crisis has "led to growing suspicion in the member states from citizens", saying it was vital to "make the work of the agencies more efficient" so as to improve this situation.
Sarvamaa highlighted the work of the Riga-based body of European regulators for electronic communications (BEREC) as being in need of improvement, adding that the agency had "too many things that didn't seem to work".
"I considered being more merciful considering BEREC is new, but there were too many fields of running the agency that were not passing the bar. We will send a strong message to every agency that they must do the best they can to properly use the money of taxpayers."
He also highlighted the importance of "opening up the barrel of some of the problems we had in agriculture and regions", adding that the commission will use "every means possible" to look at these issues.
"I am sure there is more to do," he concluded.