The protest was against the planned deportation of a group of 15 Iraqis scheduled at 8am local time, according to newspaper Göteborgs-Posten (GP) on Wednesday.
A number of the deportees are Christians, according to the UN High Commissioner for Refugees (UNHCR) and human rights organisation Amnesty International, the report said.
Police removed about 90 people from the scene and arrested 16 protesters on suspicion of police disobedience. Demonstrators blocked the entries and exits to the facility by forming human chains and with vehicles.
The protests continued on Wednesday morning at Gothenburg’s Landvetter Airport, where the flight to Baghdad was scheduled to take off, with about 150 demonstrators.
Late last month, 20 asylum seekers were deported back to Iraq from Stockholm and another six from Denmark despite heated protests against their expulsion.
According to the UNHCR, a number of the asylum seekers who were sent back belonged to religious and ethnic groups targeted by violence in Iraq. Two days before the expulsions, 70 protesters were arrested outside the facility in Kållered.
Tens of thousands of Iraqis have fled the war in their country to resettle in Sweden, with official statistics showing 117,900 people born in Iraq lived in the country in 2009, up from 49,400 in 2000.