Several UK charities raised the issue after their applications to renew their passes to the Parliament were turned down. The internal ruling has been justified as a response to the increased presence of lobbyists since the expansion of the EU last year.
The NCVO has written on behalf of UK charities to Dermot Scott, the director of the European Parliament Office in the UK, asking for an urgent review of the ruling and seeking practical advice on access under the new regime.
The NCVO warns that, with much of the legislation affecting UK charities now being initiated in Brussels, UK voluntary organisations that need to lobby the Parliament on a range of issues could now have their access to politicians restricted.
Nolan Quigley, European and international officer at NCVO, said: "This decision is a significant reversal of the European Parliament's historic commitment to participatory democracy and civil dialogue.
"How can voluntary organisations based in the UK be expected to spend their donors' money on securing permanent offices in Brussels?
"There is no transparency at all about this decision. We do not know how it was made or by whom it was taken."
The letter, signed by the NSPCC, the RSPB, the RNID and development umbrella group Bond, argues that many voluntary bodies will be unfairly affected by the ruling, while business groups are likely to have continued access through Brussels-based lobbyists.