The rules govern the way the assembly operates and have been subject to a wide ranging review overseen by UK Socialist deputy Richard Corbett.
The changes will be put to a vote in plenary in Strasbourg next week. They are designed to help make the institution operate more effectively and boost its legitimacy.
But one of the MEPs who sat on the working party that drafted the proposals has already condemned them as "undemocratic".
German GUE/NGL group member Helmut Scholz also criticised the decision not to hold a full plenary debate on the matter in Strasbourg.
MEPs will, instead, merely vote on the planned changes drawn up by the group.
Scholz, his group's shadow on what is known as "the Corbett report", told this website, "As they stand, the changes will give yet more rights to Parliament's bigger political parties and this will be to the detriment of the smaller groups. It is unacceptable and undemocratic."
Scholz was a member of the working group set up two years ago to thrash out a major revision to the rules of procedure, the key mechanism for determining Parliament's working procedures.
He briefed reporters on the content of the report at a news conference in Parliament on Thursday.
His group, he said, took issue with several aspects of the draft, saying it will lead "to an even higher concentration of powers in the bigger groups such as the EPP and Socialists."
As examples, he said that unless the report was overturned, smaller groups would find it harder to submit amendments to reports and opinions and even find it harder to submit questions to other EU institutions.
Their participation in specialised committees would be reduced and the proposals would "severely restrict" smaller group members from making written declarations and drafting resolutions.
"These changes to the rules will reduce the possibilities of intervention by smaller groups and thereby reducing pluralism.
"They would diminish the mechanisms of democratic control and scrutiny of the legislative process. This will do nothing to bridge the democratic deficit or restore public confidence in the EU."
Further comment came from GUE/NGL group leader Gabi Zimmer who, speaking at the same briefing, was equally scathing, saying the revision would reinforce the powers of the grand coalition between the EPP and Socialists.
Zimmer said, "This was supposed to improve the working practices of our Parliament but it will make things much more problematic for groups like ours."
She said an early test will be the upcoming election for Parliament's presidency.
"Gianni Pittella has said that in this election he wants an end to the grand coalition but we will have to see if that actually happens," she said.
A statement issued by GUE/NGL group Portuguese members said, "There is still time to stop and reflect" on the planned changes which will be voted on next Tuesday.
"Elected MEPs are people's representatives and not a sort of decorative furniture," it says.
"To mute their voices means to mute people's voices."