The EU on Sunday "expressed disappointment" that over a third of candidates - mainly reformers and critics of the hardline President Mahmoud Ahmadinejad - had been barred from running for parliament and said the polls were "neither fair nor free."
"The EU presidency's statement on Iran's election to parliament, which saw a high turnout and competition between different political forces, is hasty and unacceptable," official ministry spokesman Ali Hosseini said in a statement.
A partial vote count has given a landslide victory to conservatives who broadly support the president. They are set to receive 70% of seats in the 290-seat legislature. Some moderate conservatives, however, have questioned Ahmadinejad's confrontational stance with the West and his handling of the economy.
The Guardian Council, an unelected body of clerics, barred many reformers from the polls citing their lack of commitment to Islamic values.
Reformists currently hold around 40 seats in parliament.
The Interior Ministry said earlier turnout was 60-65% of the 44 million eligible voters. The results are to be officially announced by March 20.
"The EU should study the numerous signals the great Iranian people has sent to Europe and change its unfair and destructive approach to our country based on the preliminary results of the democratic election in Iran," Hosseini said.
On Friday, president Ahmadinejad accused the UN Security Council of attempting to influence the election by imposing sanctions on Iran. The resolution on a third round of sanctions over Iran's refusal to halt its nuclear program came less than two weeks before the vote.
"Before the election the enemies of our country expected the resolution to influence the bold participation of the Iranian people. However, this view was wrong," Ahmadinejad said. "The enemies of the Iranian people cannot influence the heart of our nation. This election will be a great honor for the great nation of Iran and an embarrassment for the lying [Western] media."
