The two main headquarters of the Danish daily Jyllands Posten were evacuated on Tuesday following a bomb alert.
It comes amid a crisis that erupted after the newspaper published satirical cartoons depicting the Prophet Mohammed in September.
The drawings have sparked protests, flag burning and boycotts of Danish goods throughout the Muslim world.
Danish Prime Minister Anders Fogh Rasmussen condemned the cartoons but said he could not apologise on behalf of the media.
“I would like to emphasise that in Denmark we attach fundamental importance to the freedom of expression. The freedom of expression is a vital and indispensible element in the Danish society and the Danish democracy,” he said.
While it has said it is sorry if the cartoons offend Muslims, Jyllands Posten insists it stands by its decision to publish them.
The boycott, meanwhile, continues. One dairy firm has reportedly had to lay off staff.
The boycott has been criticised by the EU’s trade commissioner, who has threatened to report Saudi Arabia to the World Trade Organisation for tacitly backing it.