By six am police moved in and towed away the cars, then arrested 25 people. This demonstration followed a similar one in Sweden's second city, Gothenburg, where 70 people were arrested after facing off with police on Tuesday near another Migration Board facility.
The protestors do not want Iraqi asylum seekers to be sent back. The United Nations High Commission for Refugees (UNHCR) also says that much of central Iraqi is too dangerous, as does Amnesty International. The Social Democrats, Greens and the Left party have criticised the government on this.
But the Swedish government, and the Migration Board, disagree. Twenty Iraqis were flown back on Wednesday and there are 3,000 facing the same deportation.
Until recently the European Court of Human Rights had been a place that Iraqis could appeal to, but on Tuesday 70 Iraqis saw their appeals turned down by the European court - and this could mean that all 2,500 who have appealed could be turned down as well.
Hanne Mathisen, spokeswoman from the UNHCR here in Sweden says that her organisation disagrees with the Migration Board on how safe the centre of Iraqi is - the UNHCR says that there's a high level of armed violence there, whereas the Swedish authorities say there is no armed conflict in Iraq any more
"The casualty levels in Iraq are very high, higher than in Afghanistan", says Mathisen. And she says that it is not just christians at risk, but other religious minorities, people with different political beliefs and those at risk because of their gender and sexuality.
The minister for migration is Tobias Billström, of the Moderate Party. He says that Wednesday's deportations is part of a system that is providing security to those in need.
"Sweden continues to offer shelter to Iraqis who need it, but there are those who have had their claim turned down, and these people have to leave - hopefully of their own accord, but if now, we have to use force."
He says that asylum seekers have to show that there is a threat directed at themselves, as individuals. Billström also says that the migration courts take information from the UNHCR on board, but that this is not enough - and that the decision by the European Court of Human Rights on Tuesday shows that the Swedish authorities are correct.