Diplomats had said that if Iran rejected the proposal, most EU countries would back a US demand that Tehran should be reported to the UN Security Council for possible economic sanctions when the International Atomic Energy Agency (IAEA) meets on 25 November.
"The EU proposal is unbalanced ... unlimited uranium suspension is unacceptable for Iran," foreign ministry spokesman Hamid Reza Asefi told a news conference.
Washington accuses oil-rich Iran of using its nuclear programme as a veil for developing an atomic arsenal. Tehran says it only wants to generate electricity.
French, British and German officials are to meet Iranian negotiators on Wednesday to discuss the European offer.
The EU "big three" have led a European effort at compromise that would avoid sending Iran's case to the UN Security Council.
The IAEA, the UN atomic watchdog body, has been investigating Iran's nuclear programme for more than two years.
It has uncovered many previously hidden activities that could be related to a weapons' programme, but has found no "smoking gun".
The EU proposal was seen as a last chance for Iran before the IAEA, the UN's nuclear watchdog, decides whether Iran is cooperating with the international community.
Tehran has long insisted it is seeking only to generate electricity and on its right to produce enriched uranium, which makes fuel for civilian reactors but can also manufacture the explosive material for atomic bombs.