Intervention from the top stops hard-liners' attempt to stall results from the capital.
Iran's supreme leader halted a recount of votes in Tehran on Thursday, effectively confirming that reformists have won control of Parliament for the first time since the 1979 Islamic revolution.
State-run Tehran radio said Ayatollah Ali Khamenei intervened after the Guardian Council, a body that supervises elections, sought his advice on a recount of votes cast in the capital during February's legislative elections.
The 12-person council, which is dominated by hard-liners opposed to the reforms of President Mohammad Khatami, had been holding up the Tehran results with allegations of widespread fraud. The council's endorsement is essential for results to be declared final.
Khamenei's intervention meant the reformists, who won 29 of the 30 seats in the capital, will be allowed to take most of those seats.
The Guardian Council told Khamenei that it had finished recounting 868 of some 3,000 ballot boxes and could not endorse the results because of discrepancies in about half the boxes, the radio reported.
Khamenei, the country's supreme authority, ordered the council to stop the recount and invalidate the votes in all boxes where discrepancies were found. "All boxes, except those in dispute so far, should be included, and the final results declared," the radio quoted Khamenei as saying.
Khamenei's order should not change the fact that reformists won an overwhelming victory. Because of the irregularities, though, Tehran's weakest winners could lose their seats, with new elections held later to fill those slots.
The Feb. 18 elections led to reformists winning a majority of seats in the 290-seat Parliament. Hard-liners control no more than 70 seats in the new Parliament.
In constituencies outside Tehran where the results have been endorsed, reformists won about 120 seats in February and between 47 and 52 seats in runoff elections last month. The runoff results have not yet been ratified.
Since the reformists' victory became clear in February, the hard-liners have been trying to regain lost ground, using their control of the judiciary. In recent weeks, the judiciary has closed 17 reformist newspapers and arrested or jailed leading Khatami allies.
The election council also annulled 12 reformist victories outside Tehran and awarded three of those seats to hard-liners. But the council's allegations of election fraud in Tehran were denied by the Interior Ministry, which jointly supervised the elections with the council.