The report gave no further information on the location or causes of deaths.
Two protesters have been killed in the south west of Iran during demonstrations according to a local politician.
The governor of Lorestan province said two protesters were killed on Saturday in the Western town of Dorud during an overnight rally.
Habibollah Khojastehpour, told state television: “On Saturday evening, there was an illegal protest in Dorud and a number of people took to the streets responding to calls from hostile groups, leading to clashes,” he said.
“Unfortunately in these clashes two citizens from Dorud were killed.”
He said “no shots were fired by the police and security forces”, and blamed “foreign agents” and “enemies of the revolutions”.
Videos appearing to show the bloodied bodies of those said to have been killed has been widely shared on social media, but there has been no independent verification of footage.
More than 400 people have been arrested across the country.
The protests are the largest to hit the country in nearly a decade and the Iranian President is due to address the nation later on Sunday.
Hassan Rouhani has called for calm, saying that people have a right to protest as long as it does not lead to violence.
He said his regime must allow “space for legal criticism” – but that “criticism is different to violence and destroying public property”.
The protests were organised in part by messages on the Telegram messaging app, which is popular in the country, with images shared on Instagram.
Access to both apps has now been blocked by authorities in an attempt to make it harder for activists to communicate with one another and share information.
Mr Rouhani also hit out at President Trump’s intervention in the protests, after he released a series of tweetswarning Tehran to respect freedom of speech.
The protests – which began on Thursday in Mashhad, Iran’s second-largest city – were prompted by discontent over the country’s weak economy and alleged corruption.
The unrest then spread to Tehran, and quickly turned against the Islamic regime as a whole.
On Saturday, tens of thousands of government supporters marched in cities across Iran in a show of support for the regime and Supreme Leader Ayatollah Ali Khamenei.
More from Iran
Iran President Hassan Rouhani: My people are free to protest
Trump warns Iran ‘world is watching’ after anti-government protests
Nazanin Zaghari-Ratcliffe ‘eligible for early release’ from jail in Iran – lawyer
Missile attack escalates tensions between Saudi Arabia and Iran
Nazanin Zaghari-Ratcliffe: Boris Johnson to voice ‘grave concerns’ during Iran trip
Nazanin Zaghari-Ratcliffe: Iran-bound Boris Johnson hopes to make progress on release
In 2009, Iran saw eight months of civil unrest when tens of thousands of people took to the streets to protest Iran’s disputed 2009 presidential election.