The move drew an angry response from the pastor in charge of the church, Per Ramsland, who said the police action violated Danish traditions of church sanctuary.
"I had never dreamed that something like this could happen," he told reporters.
Danish prison officials said the Iraqis had launched a hunger strike since being taken into custody.
"I had never dreamed that something like this could happen"
Pastor Per Ramsland,
"Since they arrived at the prison they haven't taken any meals," Lars Erik Siegmunfelt, a prison spokesman, told the AFP news agency.
He said "the majority" of the men arrested at the church had refused food.
Poul Nyrup Rasmussen, Denmark's former prime minister, also condemned the police action, saying it "went beyond the bounds of common humanity and decency".
However, Brian Mikkelsen, the country's justice minister, defended the police action, saying in a statement that "the law must be respected" and "one should not count on special treatment even if one occupies a church".
|Video of the operation showed officers beating several protesters with their truncheons [AFP]
Speaking to Al Jazeera, Jakob Hjuler Tamsmark, from Church Asylum, an organisation that helps asylum seekers, said: "Over the last years it has been documented over and over that the Danish government is basing their rejections [of the asylum applications] on a completely wrong foundation.
"We have been documenting and have been supported by the UN, by Amnesty International, and various other national organisations that the conditions in Iraq are way too dangerous to send these people to.
"We have to keep on telling people that the information they are getting from the Danish government and from the main parts of the media are lacking the details and the accuracy about the present situation in Iraq.
"The Danish population, in a broad sense, is being misled by the Danish government."
A spokesman for Copenhagen police said the 17 asylum seekers had been taken to a local police station for questioning to establish their identities and if they had a legal right to remain in Denmark.
According to Danish officials, the government has agreed a deal with Iraq over the return of more than 250 Iraqi asylum seekers, even if they do not wish to go back.
But Iraq's prime minister has denied that such a deal exists.
The policy has been criticised by the UN refugee agency and Amnesty International who say the situation in many parts of Iraq is still too unstable to guarantee the safety of returnees.