Two people were arrested following the protests that greeted Iranian President Hassan Rouhani's return from the United States after his landmark phone call with President Barack Obama, media reported Sunday.

Dozens of young Islamists had gathered at Tehran airport to vent their frustration after the moderate president spoke to his American counterpart in the first such direct discussion in more than three decades.

One protester hurled a shoe at Rouhani as he greeted a larger group of hundreds of supporters from his motorcade, but the footwear missed.

"Two people have been arrested... Anyone not wearing a shoe should have been stopped, but in fact two people were arrested, and not by us," deputy police chief Said Montazer-ol-Mehdi was quoted as saying by the ISNA news agency, apparently referring to another security service.

"An investigation has been launched," he added, without giving details about who had been arrested.

The phone call between the two leaders at the end of a five-day visit by Rouhani to address the UN General Assembly has raised hopes of a thaw in relations between the two countries, which severed diplomatic relations during the turmoil following the 1979 Iranian revolution.

Rouhani, seen as a moderate, was elected earlier this year after vowing to engage with the world on Iran's nuclear programme, hoping to lift crippling US-led international sanctions.

His decision to speak with Obama was welcomed by most Iranian media and officials, with the exception of the ultra-conservative Kayhan newspaper and other hardliners.

Foreign Minister Mohammad Javad Zarif, who accompanied Rouhani to New York and met US Secretary of State John Kerry, defended the phone call on his Facebook page, calling it a "thorn in the eye to those who wish to harm Iran and Islam."

"This is a good start to very challenging work that requires the support of everyone and the trust of the nation's people in the country's officials," he wrote.