Tehran, Iran (CNN) -- Iranian President Mahmoud Ahmadinejad, alienated from the country's supreme leader, suffered setbacks in the country's parliamentary runoff elections Saturday in what could be a sign of things to come in the Islamic republic.
Initial results showed candidates allied with Ayatollah Ali Khamenei and critical of Ahmadinejad ahead in the polling.
Sadegh Zibakalam, a professor of political science at Tehran University, said the election was "a face-off between pro- and anti-Ahmadinejad conservative factions within the ruling regime."
However, Zibakalam said Ahmadinejad still did well in critical areas like Tehran, though two winning candidates -- Ali Motahari and Ahmad Tavakoli -- are vocal critics of the president.
The runoff election was held Friday in 33 constituencies with 130 candidates competing for 65 seats in the 290-member parliament.
The first round voting was March 2 in which anti-Ahmadinejad candidates won over 180 seats, giving them a majority in the new parliament, state-run Press TV reported.
Over 48 million Iranians were eligible to vote and 64% of them cast ballots in the first round.
Ahmadinejad drew the ire of Khamenei loyalists last year when he challenged the supreme leader's authority in appointing top government officials, analysts said. But Zibakalam said he did not think the parliamentary results would make much difference in the remainder of Ahmadinejad's second and last term in office.
"His power began to weaken awhile ago after his showdown with the supreme leader," he said. "What he wanted to do was groom one of his supporters to be his replacement but I don't think he stands a serious chance of influencing the presidential elections next year.
"He tried to consolidate his power when he challenged the supreme leader and his supporters but that was the beginning of his demise," Zibakalam said.
The election for a new parliament, known as the Majlis, will also have no effect on Iran's foreign policy or its position on nuclear program. Those decisions have been and will continue to be made by Khamenei.
CNN's Reza Sayah contributed to this report