The Swedish diplomat was summoned by the ministry's director-general for Western Europe on Thursday in the absence of Sweden's ambassador to Tehran.
In a repeated and state-authorized instance of sacrilege against the Muslim holy book, two men stood outside the Swedish capital of Stockholm's central mosque on Wednesday and burned a copy of the holy book following a go-ahead given to them by a Swedish court.
The move was made to coincide with the Muslim festivity of Eid al-Adha (Feast of Sacrifice), which marks the conclusion of the annual Hajj pilgrimage that is partaken by millions of Muslims from across the world.
The act of desecration has opened the floodgates of protest across the Muslim world.
Upon summoning the Swedish diplomat, the Iranian official conveyed the Islamic Republic's strong condemnation of the act of sacrilege against the most important of Islamic sanctities.
He said Stockholm's silence and passivity had served to further embolden those, who have violated one of the fundamental and obvious principles of human rights, namely the principle of respect for religious and divine values.
The official reminded him that the act of insult had been committed at a time when Muslims were performing their Hajj rituals. It, therefore, served as nothing more than an instance of hatemongering and inclination towards aggression that had been excused through the abuse of the principle of free speech, he added.
The Iranian official said that Sweden had played host to similar injudicious actions in the past, and, accordingly, notified about the Islamic Republic's protest.
Such instances of insult would not be repeated had the Swedish authorities confronted the previous acts of desecration in time, he noted.
He concluded his remarks by repeating the Islamic Republic's intolerance of any act of violation targeting the Muslim holy book, urging Stockholm to act responsibly, effectively, and in a deterrent manner to live up to its most obvious responsibility of preventing insult against Muslims' spiritual and religious values.
For his part, the Swedish diplomat claimed that his country was against all instances of Islamophobia, saying he would notify the Swedish government about Iran's protest.