"The two men are suspected of aiding and abetting the perpetrator in connection with the shooting attacks at Krudttoenden (cultural centre) and (the synagogue) in Krystalgade," police said in a statement.
The two were arrested yesterday and will appear before a judge this morning, it said.
"Copenhagen Police does not have any further information on this subject," it said.
Police carried out a series of operations in the Copenhagen area yesterday, including an afternoon raid on an internet cafe in the inner city district of Noerrebro.
Copenhagen was hit this weekend by an assault on a cultural centre hosting a debate on Islam and free speech late Saturday, followed within hours by an armed attack on the city's main synagogue. Two people died in the attacks and five police were injured.