Iranian President Hassan Rouhani has ordered the creation of a "Coronavirus Combat and Prevention Headquarters" to be led by senior ministers and representative of Iran's Armed Forces.
President Rouhani's spokesperson Ali Rabiei has called for "more comprehensive action" and "cooperation from all citizens" to combat coronavirus in country.
The announcement came as the head of the Iranian health ministry's infectious diseases department denied reports that the city of Qom was "being quarantined" due to a Covid-19 outbreak. On Thursday, Iran reported three new cases - two in Qom - a centre for Islamic studies, attracting scholars from Iran and beyond - and one in the capital Tehran.
Reports emerged on Wednesday that two people had died in Iran after testing positive for the new coronavirus in the country's first cases, the countries health ministry had said.
The two were Iranian citizens who lived in Qom, the state YJC news agency reported.
They are also the first deaths from the Covid-19 virus in the Middle East and only the seventh and eighth outside of China, where the outbreak has killed more than 2,000 people.
Kianoush Jahanpour, a ministry spokesman, said the virus was detected in two elderly people with immunity problems in Qom, a city south of the Iranian capital, state agency Irna reported.
"Unfortunately, both passed away in the intensive care unit due to old age and issues with their immune system," Mr Jahanpour said.
He earlier said the "new coronavirus" had been confirmed in two people and that other suspected cases were isolated.
But the head of the health ministry's contagious diseases unit said the pair who died were Qom residents who were not known to have left Iran.
"These two were from Qom and visited us two days ago after falling ill," Mohammed Gouya said.
Another official in Qom said people suspected of being infected with the coronavirus would be put into quarantine in two hospitals.
"The spread of coronavirus in Qom has been controlled and we want the people not to worry about it," said Mohammadreza Ghadir, head of the city's medical sciences unit.
The new coronavirus has now claimed the lives of eight people outside mainland China.
Two have died in Hong Kong and one each in Japan, Taiwan, the Philippines and France.
The UAE last month became the first country in the Middle East to report cases of the new coronavirus strain. Egypt has also reported cases.
Iran's health sector has been hit by sanctions imposed by the US since Washington withdrew in 2018 from a landmark nuclear deal between Tehran and world powers.