Members are calling for commission safeguards against the groups' "capture" by special interests and increased transparency.
MEPs have voted in favour of freezing part of the budget for the expert groups until new rules are introduced.
The move was greeted by Brussels-based campaign group Alter-EU, saying it will "put pressure on the commission to prevent the corporate capture of EU policy preparation".
Members also want a ban on lobbyists and corporate executives sitting on expert groups in a 'personal capacity'.
MEPs say that the agendas, minutes and participants' submissions for the expert groups should also be available online.
20 per cent of the budget covering travel, accommodation and other expenses of experts coming to Brussels to advise the commission on legislative and policy initiatives will be put in reserve until the new rules demanded by MEPs are put in place.
Reacting to the move, Alter-EU researcher Yiorgos Vassalos said, ''Alter-EU welcomes parliament's move which should help resolve some serious problems that exist in EU policy-drafting. Under the current rules industry lobbyists are allowed to dominate many groups and in this way capture new draft legislation. These privileges have to be abolished and the commission should urgently produce new rules."
Alter-EU estimates that around 100 expert groups are dominated by big corporations, saying that "as a result get to co-draft policies and regulations in policy areas where they have vested interests". Such areas include finance, biotechnology, raw materials, climate, agriculture and research.
Vassalos: "Agendas and minutes of expert group meetings are rarely in the public domain. The commission should now propose new rules that effectively tackle the problems of unbalanced composition and lack of transparency."
The amendment to block funding was tabled at last week's plenary by the Greens on the report on the 2012 EU budget by the Italian S&D MEP Francesca Balzani.
It was supported by the Social Democrats, Liberals, the United Left and almost all Conservatives and Reformists.
The European ombudsman will conclude his own inquiry into whether the functioning of expert groups adheres to principles of good governance by the end of this year.