"Common sense has not prevailed in the Council, and that is worrying," Lewandowski said in a statement, referring to the EU Council of Ministers where the 28 EU member states are represented.
He said he was “puzzled” by unexpected demands for a €1 billion reduction in payments for 2014, to be deducted from the proposed €135.9 billion total.
The 2014 budget will be the first of the EU's next seven-year financial programme (2014-2020), agreed by European leaders in June after marathon talks.
The EU's draft budget for 2014, as proposed by the Commission, was already 6% lower than the one for 2013, in both commitments and payments, the commissioner stressed.
But an official position published by the Council on 2 September mentions a cut of €240.68 million in commitments and €1.06 billion in payments, compared to the Commission's initial proposal.
According to Lewandowski, the Council's position “completely ignores” the EU's heads of state and governments' decision to frontload key programmes such as the €8 billion Youth Employment Initiative and the Erasmus student exchange scheme.
The Polish commissioner slammed EU heads of states and governments for stating one day what Europe's spending priorities should be, and allowing their own national services to ignore them on the next.
“You cannot one day agree to concentrate funding of programmes in 2014 and 2015 rather than evenly spread them over the seven years of the financial period, and then conveniently ignore that agreement when discussing the 2014 EU budget,” Lewandowski asserted.
According to Lewandowski, the Council recommended cutting spending in the very areas that EU leaders, in their conclusions of June's European Council, recommended that the Union should invested in: programmes aimed at boosting Europe's businesses competitiveness (COSME) or research and innovation (Horizon 2020).
The Commissioner also warned against Council recommendations for a 7% reduction in staff budget, arguing that cuts to administrative support would slow down expenditure on research and innovation programmes.
Commission sources told EurActiv that austerity was hitting hard at research and innovation, because the costs had risen enormously, while budgets had been slimmed down.
Lewandowski said he hoped that the conciliation procedure following the European Parliament's position on the 2014 budget would enable the institutions “to reach an agreement that is sensible, that does not go against the wishes of Europe's national leaders and that will give Europe's economy and confidence a badly needed boost".