Alireza Ronaghi, Al Jazeera's correspondent in the capital, Tehran, said: "[The Guardian Council has] given in from pressure. It appears Ayatollah [Ali] Khamenei, the supreme leader, has forced them to comply with the request."
The council has said a recount of some disputed ballot boxes may lead to changes in the candidates' tally.
Mousavi had asked for the election result to be annulled.
Hundreds of thousands of people have taken to the streets of cities across Iran since the result, with both Ahmadinejad and Mousavi supporters planning further rallies in Tehran, the capital, on Tuesday.
But Mousavi has called on those who support him not to attend a planned rally in the capital, his spokesman said.
"Mousavi ... urged his supporters not to attend today's rally to protect their lives. The moderates' rally has been cancelled," the spokesman said.
Iran's culture ministry has banned foreign journalists from covering "unauthorised" rallies, meaning those loyal to Mousavi.
Also on Tuesday, the Iranian authorities arrested two prominent reformists, Saeed Hajjarian and Mohammad Ali Abtahi, their aides said.
Iranian state television also reported that the "main agents" in the clashes had been arrested with explosives and guns in their possession.
Press TV, Iran's English-language television station, reported the arrests in a breaking news headline, but did not give details of how many people had been arrested or when.
The semi-official Fars News Agency quoted a senior police official as saying that "anti-revolutionary" activists had been arrested with weapons and explosives, in what appeared to be the same police operation.
Deaths in Tehran
An Iranian state radio channel had reported in the day that seven people were killed after an attack on a military post close to a rally that took place on Monday.
The violence occurred in Tehran's Azadi Square, Radio Payam reported.
|Scores of people have been hurt after police moved to break up the protests [AFP]
"Several thugs wanted to attack a military post and vandalise public property in the vicinity of Azadi Square," the radio said, referring to the site of the rally.
"Unfortunately, seven people were killed and several others wounded."
Ronaghi reported that protests on such a scale in Iran were unprecedented.
"The anger and hatred in the eyes of both sides - whatever the result, it will anger some people," he said.
"The police have been trying to remain as civilised as possible, but not everyone is listening to police commanders.
"It's not easy to calm them down. What happens when the chain of command is broken, when both sides are going rogue and not listening to their commanders? This is going be a very dangerous situation," Ronaghi said.
Ahmadinejad in Russia
The news of the deaths came as Iran's president arrived in Russia for a security conference, despite the popular protests at home against a vote in which the authorities declared him the winner.
Ahmadinejad landed in Yakaterinburg for the Shanghai Co-Operation Organisation (SCO), in which Iran has observer status.
"We welcome the fact that elections took place, we welcome the new president on Russian soil and see it as symbolic that he made his first visit to Russia," Sergei Ryabkov, Russia's deputy foreign minister, told reporters after Ahmadinejad's arrival.
"This allows hope for progress in bilateral relations," he said.
Ahmadinejad's trip had been scheduled for Monday but he postponed it in the wake of the protests.