The cause of the blast, which occurred around 10:00 pm (2000 GMT) at the agency's headquarters in the capital's Osterbro district, was not immediately known, Copenhagen police said.
But they were considering it as a possible criminal act.
"We are investigating this as a suspicious occurrence," a police duty officer told AFP.
"It is too early to say now who is behind the explosion," Copenhagen police inspector Jorgen Bergen Skov said in a statement.
Investigators and bomb sniffer dogs were at the scene on Wednesday, police said.
Windows were smashed and the front of the building was torn apart.
Two people were inside at the time of the blast but they were not injured, a police spokeswoman told AFP, adding that employees have been asked to work from home on Wednesday.
Danish Tax Minister Morten Bodskov told the Ritzau news agency it was "pretty obvious the facade has been blown up" deliberately, calling it a "totally unacceptable act".
"Copenhagen police are conducting an investigation, but if anyone knows anything they should come forward," he said.