"In total, 26 people were deported, 20 from Sweden and six from Denmark" on board a plane travelling to Baghdad on Wednesday, the Stockholm police said in a statement.
Ahead of the deportations, human rights groups and the UN refugee agency UNHCR had called on the countries to rethink the move, insisting it was too dangerous to send the rejected asylum seekers -- reportedly some of them Christians and homosexuals who risk persecution -- back to Iraq.
"The deportations were in accordance with expulsion orders from the Swedish National Migration Board (Migrationsverket), immigration courts and ordinary courts, which were handed over to police authorities," police said.
Earlier on Wednesday, police detained 25 people who protested outside an asylum seeker detention center near the Swedish capital. The protesters were reportedly part of a group of up to 100 people trying to block the mass deportation.
The Swedish section of Amnesty International had asked Immigration Minister Tobias Billström to halt the return of Iraqis, while the country's Christian Council also called for a suspension of deportations to Iraq, especially of members of ethnic or religious minority groups in that country.
Their calls were echoed by the UNHCR, which on Tuesday expressed strong concern at reports that Sweden planned to send Iraqis back to Baghdad despite repeated warnings that conditions there are unsafe.
On Tuesday, 70 people were detained after demonstrating outside offices of the Swedish Migration Board near the southwestern city of Gothenburg and amid rising criticism of the deportations.
Swedish immigration authorities ruled in 2007 that "there is no armed conflict in Iraq" and that it was therefore acceptable to return Iraqi citizens to their country. The ruling meant that Iraqis were no longer automatically granted asylum.
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 Scandinavian country in 2009, up from 49,400 in 2000.