Iranian Foreign Ministry Spokesman Bahram Qasemi was quoted by state news agency IRNA as saying that the Swedish envoy in Tehran had been summoned in protest on Monday.
"In the meeting, the Islamic Republic of Iran voiced strong protest against the action taken by the Swedish government to grant citizenship to an agent of Mossad who has confessed to participating in the assassination of Iranian scientists," Qasemi stated.
"We have been in regular contact with Iranian representatives, requested access to Djalali and presented Sweden's view on the death penalty, which we condemn in all its forms. Our demand is that the death penalty not be carried out," a Swedish spokeswoman said.
Qasemi considered Sweden's move "questionable and unfriendly," and added that Tehran "could not accept the foreign nationality" of the detainee.
Djalali was on a business trip to Iran when he was arrested and sent to the Evin prison.
Seventy-five Nobel Prize laureates wrote a petition to Iranian authorities last year, requesting the release of Djalali so he could "continue his scholarly work for the benefit of mankind."
He was allegedly held in solitary confinement for three months and tortured, human rights group Amnesty International has said.