The affair, which dates to 2021, has been a long-running source of embarrassment for the Danish government.
"I cannot defend this decision," said Prime Minister Mette Frederiksen, whose administration has taken a hard line against migration and asylum requests.
In November 2021, alleged pirates on a small boat in the Gulf of Guinea opened fire on a Danish naval helicopter on anti-piracy patrol.
Four men on the boat were killed in the exchange, a fifth went overboard, and three were arrested before being released at sea.
But another man, who presented himself as being from Nigeria and going by the name "Lucky", wasn't released because his leg had to be amputated on the spot after he was hit.
He was later transferred to Denmark for further treatment.
"He doesn't belong here. If he's here, it's solely because of international obligations," Frederiksen said during a press conference.
Once in Denmark, "Lucky" was found guilty of putting the lives of Danish soldiers in danger, but wasn't sentenced to prison.
He applied for asylum while in a centre waiting to be sent back to Nigeria.
His lawyer didn't respond to requests for comment on how he was granted asylum.
The Gulf of Guinea, which extends for 5,700 kilometres (3,350 miles) from Senegal to Angola, was once plagued by piracy but is now much safer thanks to joint efforts from European navies and local forces.
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