English-language Press TV reported the Guardian Council's rejection of an annulment on Tuesday.
On Monday, it had conceded there had been voting irregularities in 50 districts, including local vote counts that exceeded the number of eligible voters.
But it said they were not enough to affect the overall result and incumbent Mahmoud Ahmadinejad had indeed won by a landslide.
The council's spokesman said most of the irregularities happened before the election, not during or after voting.
In a letter to the council, Mr Karoubi said: "Instead of wasting time on recounting some ballot boxes... cancel the vote."
On Monday 1,000 people gathered in Haft-e Tir Square in the capital Tehran despite a warning from Iran's Revolutionary Guards, an elite armed force, against holding unapproved rallies against the election results.
Iranian riot police in Tehran observe as 1,000 attend rally
Basij militiamen wielding clubs were brought in to reinforce the police.
The protests in the last 24 hours are smaller than they have been over the past 10 days, amid the strong security presence on the streets.
BBC Middle East editor Jeremy Bowen said the protesters are talking about finding other ways to show their opposition, including strikes or civil disobedience.
'Beginnings of change'
A spokesman for the US government said it "would not endorse" general strikes.
But he added: "We've seen the beginnings of change in Iran."
British Prime Minister Gordon Brown told the BBC: "We want a very good relationship with the Iranians, we also respect the fact that it's for the Iranian people themselves to choose who their government is.
"But when there is a sign of repression or where there is violence that's affecting ordinary people in the streets, we have a duty to speak out and to say we want Iran to be part of the world, we don't want Iran to be isolated from the world."
On Friday Ayatollah Ali Khamenei banned protests, prompting street violence in which at least 10 people died.
UN Secretary General Ban Ki-moon has called for an end to the street violence, and threats of violence.
Mr Ban urged the authorities in Iran to respect fundamental civil rights, "especially the freedom of assembly and expression", and end arrests.
A spokesman for Mr Ban said he had been following the situation in Iran with "growing concern" and was dismayed by the use of force against civilians.
Call for dialogue
He called on Iran's government and opposition to resolve their differences peacefully through dialogue and legal means.
Ban Ki-moon has damaged his credibility in the eyes of independent countries
Iranian foreign ministry spokesman
"He urges an immediate stop to the arrests, threats and use of force. The secretary general reiterates his hope that the democratic will of the people of Iran will be fully respected," a statement read.
But Iranian foreign ministry spokesman Hassan Ghashghavi said: "These stances are an evident contradiction of the UN secretary general's duties, international law and are an apparent meddling in Iran's internal affairs.
"Ban Ki-moon has damaged his credibility in the eyes of independent countries by ignorantly following some domineering powers which have a long record of uncalled-for interference in other countries' internal affairs and colonisation."
A pro-government rally proposed by students to be held outside the British Embassy has been called off after they were denied a permit.
Severe reporting restrictions placed on the BBC and other foreign media in Iran mean protest reports cannot be verified independently.
Election results show Mr Ahmadinejad won the 12 June election by a landslide, taking 63% of the vote, almost double that of Mir Hossein Mousavi, his nearest rival.
An independent British analysis of the disputed election results has found irregularities in the reported turnout, as well as "implausible" swings in the vote in favour of Mr Ahmadinejad.
Analysts from St Andrew's University and the Chatham House think-tank said votes in favour of Mr Ahmadinejad in a third of the provinces would have required an "unlikely scenario" of voting patterns.
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