"The actions last night by a group of radicals in Tehran and Mashhad leading to damage at the Saudi embassy and consulate are totally unjustifiable, as the buildings should be legally and religiously protected in the Islamic Republic of Iran," Hassan Rouhani said, quoted by the official Irna news agency.
At least 44 people were arrested late on Saturday for storming the diplomatic missions in Tehran and Mashhad after Saudi Arabia announced it had executed 47 people.
UN chief 'deeply dismayed', urges calm
UN chief Ban Ki-moon said he was "deeply dismayed" by Saudi Arabia's execution of 47 people including a prominent Shia cleric, whose death sparked violent protests in Iran, a spokesman said.
Following his execution on Saturday, angry crowds hurled petrol bombs outside the Saudi embassy in Tehran before storming the building.
Protests also broke out in at least one city in Saudi Arabia's Eastern Province, as well as in Iraq and Bahrain.
Ban's spokesman said the UN chief was "deeply dismayed over the recent execution by Saudi Arabia of 47 people."
Deploring the violence outside the Saudi embassy in Tehran, he called for "calm and restraint" and urged "all regional leaders to work to avoid the exacerbation of sectarian tensions," his spokesman said in a statement.
Saudi Arabia's interior ministry said the executed men had been convicted of adopting the radical "takfiri" ideology, joining "terrorist organisations" and implementing various "criminal plots."
Ban was quoted as restating "his strong stance against the death penalty."
