MEPs have refused to grant budgetary discharge for three European 'joint undertakings', or projects.
This includes the EU budget line for 2014 for the controversial ITER nuclear fusion project.
The ITER project is already said to be three times over budget and some MEPs have now called for its suspension.
The other two projects are ARTEMIS, the joint undertaking for embedded computing systems, and ENIAC, a partnership focusing on nanoelectronics.
A report voted by Parliament's budgetary control committee highlights concerns with "cost overruns, delays and mismanagement."
Parliament is responsible for granting discharge to the annual EU budget and where concerns about budgetary irregularities are raised, MEPs may withhold or postpone the discharge of sections of the budget.
Reaction from MEPs to the decision to withhold discharge for the three projects was swift.
Green budgetary transparency spokesperson Igor Šoltes said, "The ITER nuclear fusion project is a costly white elephant for which the European taxpayer is being left to foot the bill. MEPs have today raised serious concerns with the project, which relies on the EU budget for a large proportion of its funding."
He pointed out that members of the committee had cited "concerns about further future cost overruns, delays, mismanagement in the ITER agency and the negative impact on other EU budget lines.
He added, "Setting aside the serious doubts about the viability of the project, it is clear that its ballooning budget does not represent a reasonable use of taxpayers' money and we hope Parliament's plenary will replicate the committee vote and withhold granting a discharge to ITER when the vote takes place."
Greens/EFA group Co-Chair Rebecca Harms said, "The ITER project is turning into a farce.
"Beyond the unacceptable ballooning budget for ITER and how the project is run, there is the inescapable reality that nuclear fusion is a pipe dream.
"Even if the disappointing ITER project were to produce some results on its further delayed schedule, we would remain decades away from commercial application."
Parliament's rapporteur on the budget discharge, Marian-Jean Marinescu, underlined the need for better auditing generally.
"Clarification is needed for some questions considering the administration of these public-private partnerships. As ARTEMIS and ENIAC merged in June 2014, it is of great importance that the accounts are clear for future discharges and that no questions are left open", said the deputy, who is responsible for budget and structural policies for the EPP group.
He added that he was particularly concerned about the quality of the audit reports on public-private partnerships.
"The European Court of Auditors should provide Parliament with more detailed information in its future reports, including concrete provisions regarding the private partners' contribution evaluation procedure", said Marinescu.
On ITER, he noted that, "This is a very important European project and has been making progress over the last period. We are waiting for the decision of the ITER council regarding the future schedule, including activities and financing needs."