Opposition websites reported police had fired into crowds of demonstrators in central Tehran during Sunday's protests and witnesses said dozens of protesters were wounded in the police crackdowns.
The reports could not be independently verified because foreign media are banned from covering protests.
Ahmad Reza Radan, Iran's deputy police chief, said that more than 300 protesters had been arrested and acknowledged that "several people" had been killed, but said police had not used guns to contain the protests.
Referring to four of the deaths, Radan said: "One fell off a bridge, two died in car accidents and one was killed by a bullet."
"As the police was not using firearms this [death] is suspicious and it is being investigated," he said.
Opposition leaders criticised the government for the killings in what are some of the bloodiest confrontations in Iran since the demonstrations that followed the disputed June 12 presidential poll.
"What has happened to this religious system that it orders the killing of innocent people during the holy day of Ashoura?" Mehdi Karroubi, one of the defeated reformist candidates in the election, said in a statement reported on the Jaras website.
'We fight and we die'
Video footage posted on the internet, said to be from the protests, showed protesters running away from riot police or Basij militias on motorbikes.
Witnesses said protesters fought back against the security forces, pelting them with stones and chanting: "We fight and we die to get back Iran."
Several policemen were reportedly beaten up and their pick-up trucks set on fire, witnesses said.
The Jaras website said that unrest spread to other parts of Iran, including the holy city of Qom, Shiraz, Isfahan, Najafabad, Mashhad and Babol.
Payam Akhavan, an international law professor based in Montreal and the co-founder of the Iran Human Rights Documentation Centre, said that Sunday's protests were a further manifestation of the discontent felt over the June poll.
He also highlighted that the protests were taking place around the festival of Ashoura, a significant religious commemorations for Shia Muslims that commemorates the seventh century death of Prophet Muhammad's grandson.
"It's clear that the protests against the regime encompass a very broad cross-section of Iranian society, including devout Muslims"
Co-founder of Iran Human Rights Documentation Centre
"The regime has tried to portray the Green [opposition] Movement, the protests, as a very limited segment of Iranian society - middle class, secular students in Tehran," he told Al Jazeera.
"But now it's clear that the protests against the regime encompass a very broad cross-section of Iranian society, including devout Muslims."
But Mohammad Marandi, a professor at Tehran university, played down the significance of the protests.
"Initially after the elections a lot of people in Tehran did believe there were irregularities in the poll, but after a period of time when Mousavi was unable to provide any form of evidence, that belief gradually disappeared," he told Al Jazeera.
"The opposition is very much fragmented now and those people that you do see demonstrating are a segment of the reformist movement. Other segments of the movement have distanced themselves from Mr Mousavi over the last few months.
"For example a reformist faction in parliament no longer supports the Green Movement as it stands today. The group that rallied yesterday [Sunday] was extremely violent and extremely small."
Mirandi also said that the recent protests were being organised from abroad, a sentiment frequently stressed by the Iranian government.
"They are largely being orchestrated from abroad, they are orchestrated from television networks that are being beamed in from the United States and Europe," Mirandi told Al Jazeera.
|The protests are some of the worst since those following the disputed presidential poll [EPA]
"The important thing is that initially the protests against Mr Ahamdinejad were more homegrown ... but gradually the pro-American opposition, the opposition supported from outside the country, began to have a greater role."
But Trita Parsi, the president of the advocacy group the National Iranian American Council, rejected that assessment.
"This is a movement that is homegrown, that is finding its inspiration from what is taking place inside the country," he told Al Jazeera.
"There is no evidence or any clear indication that they will be taking any particular orders or money from outside.
Iran's government has been criticised internationally for its clampdown on the protest. In the US, the White House strongly condemned "violent and unjust suppression" of civilians.