Officers had been given orders to “show restraint”, the chief of police said.
Videos posted online on Sunday recorded what appeared to be gunfire and showed an injured woman being carried away.
Protests erupted on Saturday, after Iran admitted firing missiles by mistake at the Ukraine International Airlines jet that crashed near Tehran.
All 176 people on board Flight PS752, mostly Iranians and Canadians, were killed.
For the first three days after the crash, Iran denied that its armed forces had shot down the plane and suggested there had been a technical failure.
The admission of responsibility, which came in the face of mounting evidence, provoked widespread anger in Iran against the ruling establishment.
Days earlier, Iranians had been united in grief over the killing of General Qasem Soleimani, their country’s second most powerful man, in a US drone strike in Iraq.
What happened at the protests?
Sunday’s demonstrations went on late into the night, as people vented their fury against the Iranian government and the powerful Revolutionary Guards, who shot down the Ukrainian plane.
There were reports that a number of people were injured when security forces broke up a protest in Tehran’s Azadi Square, during which people chanted “death to the dictator” – a reference to Supreme Leader Ayatollah Ali Khamenei.
One video posted on social media allegedly shows members of the paramilitary Basij Resistance Force, which is often used to suppress domestic dissent, attacking protesters in the area. What appears to be gunfire can be heard.
Another video shows an injured woman being carried away by people who shout that she has been shot in the leg. A pool of blood is seen on the ground.
Despite such footage, Tehran police chief Brig-Gen Hossein Rahimi insisted that his officers did not fire live ammunition at protesters, as security forces did when cracking down on mass anti-government demonstrations in November.
“The police treated the people who had gathered with patience and tolerance,” he said, before warning that “those who intend to manipulate the situation” would face consequences.
Iranian government spokesman Ali Rabiei meanwhile dismissed as “crocodile tears” US President Donald Trump’s expressions of support for the protesters.
The captain of the national men’s volleyball team, Said Marouf, wrote on Instagram about “oppression” in Iran. In an apparent reference to the shooting down of the plane, he said he hoped Iran has seen its “last show” of “deceit and stupidity”.
And one of Iran’s most famous actresses, Taraneh Alidoosti, posted that Iranians were being treated not as citizens but as “hostages”.
Over the weekend Iran’s only female Olympic medallist said she had defected.
What’s the latest on the Flight PS752?
Canadian Prime Minister Justin Trudeau told a memorial service for the 57 Canadian victims that their country “will not rest until we get the accountability, justice, and closure that the families deserve”.
The Iranian government meanwhile denied there had been a cover-up.
“On these sad days, numerous criticisms were raised against the country’s officials; some of us have been accused of lying and secrecy. But honestly it was not like that,” spokesman Ali Rabiei told reporters on Monday.
“The reality is that we did not lie,” he added, blaming “a lack of valid information” and also “the US’s psychological warfare” for his own and other officials’ denials that the plane was shot down.
Mr Rabiei insisted that senior officials, including President Hassan Rouhani”, did not know that missiles had been launched at the airliner until Friday evening.
He also praised Revolutionary Guards Aerospace Commander Brig-Gen Amir Ali Hajizadeh for his “honest” and “bold” acknowledgement that his forces were responsible for the tragedy.
Gen Hajizadeh said on Saturday that Iran’s air defences were on the highest state of alert because the Revolutionary Guards had just fired ballistic missiles at US bases in Iraq in retaliation for the killing of Qasem Soleimani.
The operator of a missile defence system near Tehran’s airport mistook Fight PS752 for a US missile and due to problems with a communication system was unable to contact the command centre, according to the general.
“He had 10 seconds to decide,” he added. “He could have decided to strike or not to strike, and under such circumstances he took the wrong decision.”
Gen Hajizadeh said he had informed “officials” on Wednesday about the unintentional strike.
President Rouhani called the incident an “unforgivable mistake” and promised that those responsible would be identified and prosecuted.
In a separate development on Monday, the UK Foreign Office summoned Iran’s ambassador in London following the detention of his British counterpart in Tehran after he attended a vigil for victims of the Ukrainian plane crash.
The CEO of Canadian company Maple Leaf Foods, Michael McCain, meanwhile criticised the US government for escalating tensions in the Middle East in the days before the crash, in which he said a colleague lost his wife and family.