The three MEPs, all from different parties, warned that that the latest version of the accord "is not compatible with existing EU Treaties."
Eurozone leaders decided to draw up a new accord, which sets up tighter limits on budget deficits and is supposed to pull the 17 countries that use the euro closer together, at a summit in December in the hope that it would help the currency union pull out of its worsening debt crisis.
They were forced to resort to a separate accord after the U.K. blocked changes to existing EU treaties. All nine other EU countries that do not use the euro have supported the new accord in principle.
But the European Parliament in particular is concerned that the separate treaty sets up parallel structures within the EU, disempowering elected lawmakers and the European Commission.
"The draft does not guarantee that any decision to implement the new agreement would be taken via the normal procedures laid down in the EU treaties to ensure proper democratic scrutiny and accountability," Elmar Brok, a member of the centre-right European People's Party; Roberto Gualtieri from the Socialist party, and Guy Verhofstadt, a liberal, said in a joint statement.
Their warning underlines a trend that has become more and more pronounced as the eurozone's debt crisis has intensified over the past two years: important decisions are made by heads of state and government at EU summits — often dominated by the leaders of France and Germany — and then presented as a take-it-or-leave-it deal to national parliaments.
The parliamentarians are concerned that most of the amendments they made to the previous draft — stressing the role of the Parliament and the Commission — were not taken up in the latest version. A roadmap toward eurobonds, debt instruments backed by the eurozone as a whole, also did not make it into the draft.
There were few major changes to the new rules established in the accord. One point of contention is the number of countries that have to ratify the new treaty before it comes into force.
The first draft, circulated before Christmas, stipulated that only eight countries had to ratify the treaty to bring it into existence. A second draft increased that number to 15, while the latest version takes it back down to 12.
Even though the treaty would only apply to the countries that have ratified it, a lower threshold for bringing it into force makes it easier for countries to set up new structures.
However, a spokesman for Verhofstadt stressed that this section was not a "make-or-break" issue.
The next round of negotiations will take place on Thursday morning and the Parliament will adopt its official position on the new accord next week.