"It has been decided to open the mosques across the country... giving worshippers the chance to perform their daily prayers while respecting the required (hygiene) rules," Rouhani said in a televised speech.
He said the reopening of mosques for daily prayer "would not only be in white zones," but did not elaborate on when the eased measures would take effect.
Authorities had progressively closed mosques across Iran after confirming the first coronavirus infections in February.
Mosques in areas falling into the white category were allowed to reopen their doors to the public during the fasting month of Ramadan – April 25 to May 24 – but only for individual prayers.
For Eid al-Fitr, the holiday marking the end of Ramadan, collective prayer was permitted in some areas.
Rouhani also said that shopping malls would be able to stay open beyond the 6 p.m. closing time imposed as part of the curbs.
The president also warned the population against believing that the country was rid of the virus, emphasizing that it was here to stay.
He urged citizens to respect the rules on social distancing fastidiously.
A further 57 people who tested positive for the virus died over the last day, the Health Ministry said Saturday, taking the total confirmed death toll to 7,734.
The official figures show a renewed acceleration in virus cases since early May.
The ministry announced 2,282 new confirmed infections on Saturday, taking the total number of declared infections since February to 148,950.
Ministry spokesman Kianoush Jahanpour said that the southwestern province of Khuzestan was still classified as “red” due to the higher number of infections and deaths, while seven other provinces were at risk.
The Health Ministry has divided the country into white, yellow, and red areas based on the number of cases and fatalities.
On Friday, authorities announced new confirmed cases in the previous 24 hours had totaled 2,819, a near two-month high.
Authorities are taking tougher measures to ensure health regulations are observed, such as barring people from buses and metro trains if they do not wear face masks.
Alireza Zali, the head of the Coronavirus Taskforce of Tehran, said the situation in the capital was “still not favorable,” adding that the gradual easing of curbs should be accompanied by a “more serious observance” of the rules.
Reuters and AFP contributed to this story.