The policy is contentious and a proposal to filter WhatsApp has caused a rupture between Rouhani's administration and a 13-member committee responsible for Internet censorship.
The reformist Sharq daily reported that Rouhani has ordered a stop to a proposed access ban on the free messaging service.
"The issue of banning WhatsApp was raised. The president has ordered a halt on (banning) the site," Telecommunication Minister Mahmoud Vaezi was quoted as saying.
"Until the time that we have a replacement for these sites, the government opposes filtering them," he added.
According to an official at the telecommunication ministry, the ban was approved by the censorship committee but not yet implemented.
Government officials have voiced support for lifting the wider ban on social media websites.
Rouhani has promised greater tolerance on social, cultural and media issues a vow that helped him beat his conservative opponents in the presidential election last year.
But the government has faced resistance from hardliners, who oppose a reversal on such censorship.