Iran, one of the Middle Eastern countries hardest hit by the pandemic, will be divided up into white, yellow and red regions based on the number of infections and deaths, Rouhani said, according to the presidency's website.
Activities in each region will be restricted accordingly, so an area that has been consistently free of infections or deaths will be labelled white and mosques could be reopened and Friday prayers resumed, Rouhani said.
He said the label given to any region in the Islamic Republic could change and he did not specify when the colour-coding programme would come into force.
Deputy Health Minister Iraj Harirchi said in an interview with state TV on Sunday that 116 counties in the country could be considered white at the moment and 134 yellow.
Iranians have returned to shops, bazaars and parks over the past week as the country eases coronavirus restrictions, with the daily increase in the death toll below 100 since April 14.
The toll rose by 60 over the past 24 hours to 5,710, with 90,481 confirmed cases, Health Ministry spokesman Kianush Jahanpur told state TV on Sunday.
Seeking a balance between protecting public health and shielding an economy already battered by sanctions, the government has refrained from imposing the kind of wholesale lockdowns on cities seen in many other countries.
But it has extended closures of schools and universities and banned cultural, religious and sports gatherings.
Iranian Foreign Minister Mohammad Javad Zarif had a phone call with United Arab Emirates Foreign Minister Abdullah bin Zayed Al Nahyan on Sunday and discussed the battle against the spread of the coronavirus and regional developments along with passing on a congratulatory message for the beginning of the holy month of Ramadan.