Protesters threw eggs at the door of the Swedish Institute of International Affairs where Mottaki was due to deliver a speech, and shouted slogans denouncing the Iranian regime.
The group also called for the release of political prisoners.
A large police force was on hand to prevent the demonstrators from entering the building.
In his address, Mottaki stressed that Iran's nuclear programme was "peaceful" and posed "no threat to international peace and security."
The UN Security Council imposed new sanctions on Iran in March and has demanded the country suspend its uranium enrichment programme.
The United States, among others, has accused Tehran of developing a nuclear weapons programme alongside its nuclear power programme, which Iran has denied.
"When nothing is wrong, you cannot make any punishment," Mottaki said.
"Despite doomed attempts to isolate the Islamic Republic of Iran, any security arrangement in the region will not succeed without the participation of Iran," he added.
Mottaki was scheduled to meet with Swedish Foreign Minister Carl Bildt and Deputy Prime Minister Maud Olofsson later on Monday.
The visit to Sweden of the Iranian foreign minister also led to protests from a number of Swedish organizations.
On Monday, several newspapers published a joint article penned by representatives of Swedish publishing and writers' organizations in which Carl Bildt and Maud Olofsson are urged to issue a strong protest against the Iranian regime's mistreatment of women pushing for equal rights in the country.
Two weeks ago, two leading figures in the Iranian women's movement were each sentenced to three years in prison for "conspiracy with the intention of damaging national security".
The two women, Parvin Ardalan and Nooshin Ahmadi Khorosani, were among the instigators of a campaign for equal rights which managed to gather one million supportive signatures.
The authors of Monday's article called for the verdict against the women to be overturned and for Foreign Minister Bildt and Deputy Prime Minister Olofsson to encourage the EU to take action on their behalf.
Several Iranian women's organizations in Sweden have condemned the Swedish government for allowing Mottaki to visit. They have also called for Sweden to break off all political and cultural ties with Iran.