The 59 unarmed protesters remained on the Lufthansa aircraft more than 10 hours after other passengers and crew had disembarked from the flight from Frankfurt and the pilot disabled the plane.
"We want the European Union to remove the Islamic leaders from Iran," Armin Atshgar, a protester, said by mobile phone. "We want to remove the mullahs from power."
Atshgar, who described himself as a member of Anjomane Padeshahi, a group advocating the restoration of Iran's royal family, ousted in the 1979 Islamic revolution, said Belgian foreign ministry officials had boarded the plane and spoken to the protesters.
"We are talking to these people. They are non-violent and it's not a hijacking," a foreign ministry spokesman said.
Atshgar, who said he held a Belgian passport, said he and his fellow protesters would not leave the aircraft until they had spoken to a member of the European Parliament.
"We are not going to leave this plane until they listen to what we want," he said.
"We want the European Union to remove the Islamic leaders from Iran"
Protester Armin Atshgar
But two of them later left the plane. One was diabetic. The other, suffering from back pain, was taken away in an ambulance.
Atshgar said children and pregnant women were among those on board, adding that the mood was calm and safe.
He insisted the European Union should help oust Iran's leadership.
"We want to say to all the world's leaders, especially from the European Union, Belgium, France, Britain, Germany and the Netherlands, 'hands off and stop supporting this Islamic rule by removing it from Iran'," Atshgar said.
The EU is negotiating to try to persuade Tehran to curtail sensitive nuclear work which could help it produce a bomb, in return for trade and security benefits.
Police spokeswoman Els Cleemput said the protesters all had European passports but they were probably all of Iranian origin.
A Lufthansa spokesman said the plane, a Boeing 737, had landed in Brussels's Zaventem airport with 103 passengers and crew.
Police said the protesters had refused food, but it was not clear if they were on hunger strike.
Air traffic was normal at Brussels National Airport and another plane was allowed to dock in the next bay.