MEPs sitting in the Belgian capital said they had been provided with no satisfactory answer over how they will cover the loss of Britain's membership fee at a time when many European economies are struggling.
One worried German representative accused colleagues of buring their heads in the sand, sayin: "When it comes to revenue and expenditure we can’t just say it’s business as usual."
During the meeting MEPs also listed halting the rise of politicians like Marine Le Pen and Geert Wilders as one of the top challenges facing the bloc in 2018.
And they could not resist taking a pop at Britain as they put forward their proposals for the EU’s spending priorities, accusing successive UK Governments of holding them back.
MEPs are discussing the next EU budget today
But it was their worried comments about Brexit which were the most illuminating, with EU politicians seemingly at odds over where to find the cash to cover Britain's decision to leave.
German MEP Jens Geier said: "We can’t discuss this without talking about Brexit and the possible consequences for the EU budget. The radical changes that are going to occur when the second biggest net payer disappears are something that should at least be dealt with.
"When it comes to revenue and expenditure we can’t just say it’s business as usual."
Slovenian Patricija Sulin added: "I am still waiting for an answer to the question how are we going to close the gaps when the United Kingdom leaves? This 16 billion euros that the UK is paying into the budget annually is going to need to be replaced."
The report was presented by Romanian MEP Siegfried Mureşan
German MEP Jens Geier said the EU cannot presume it is 'business as usual' after Brexit
The meeting also heard that on top of that the EU budget will need huge increases in the coming years if Brussels is to fulfil its defence ambitions, but that voters will not accept money being syphoned off from social projects to pay for troops.
But Polish MEP Jan Olbrycht urged colleagues not to panic over Brexit, saying that the figures being bandied about for the size of the funding shortfall were exaggerated.
He told the chamber: "The gap after Brexit is not 15 billion euros, its five billion by the time you take British payments, the rebate and expenditure. We cannot exaggerate, so the real problem is are the member states ready to repay this five billion?"
Representatives on the EU’s budget committee met at the European Parliament earlier today as the legislative process for passing the 2018 budget got underway.
Romanian MEP Siegfried Muresan, who is leading the negotiations for the parliament, presented a draft report laying out where it would like to see European taxpayers’ cash spent.
He told the meeting that the effect of Brexit on next year's budget will be "close to zero" because the UK will still be a member, but said MEPs must carefully watch how the issue of future contributions unfolds during the upcoming divorce talks.
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Elsewhere in his proposal he said that the committee “welcomes the important role played by the EU budget in delivering concrete answers to the challenges the EU is facing”.
He said it “stresses that jobs, economic growth, migration, security and tackling populism are the main concerns at EU level and that the EU budget remains part of the solution to these issues”.
But in a nod to growing concerns about globalisation a passage was inserted warning Brussels that “obtaining sustainable progress…will not be possible should EU citizens feel unsafe or insecure”.
And the committee could not resist having a pop at Britain over its decision to leave the club, suggesting that the budget will be increased significantly once Brexit is complete.
They noted that “the United Kingdom’s withdrawal from the EU will provide an opportunity to address the long-standing issues which have prevented the EU budget from reaching its real potential, especially as regards the revenue side of the budget”.
The proposed budget, which it is believed will amount to around 150 billion euros (£130bn), has a number of hoops to jump through before it is passed into law.
It has to be agreed by the full European Parliament and the EU Council, which is made up of the 28 heads of Government of the member states each of which wields a veto.