"Rocks and then a burning object were thrown through the window," a police spokesman told AFP. "Two rooms on lower floors were damaged but the fire was put out quickly."
Like many other German newspapers, Hamburger Morgenpost has printed cartoons of French satire magazine Charlie Hebdo after the deadly attack on Wednesday in Paris.
A police spokeswoman said that an incendiary device was thrown at the newspaper building in the night and documents were burned inside. Two suspects were arrested near the crime scene because they behaved in an unusual manner, she added.
The newspaper said on its web page that there were no people inside the building when the attack happened. Whether the arson attack was connected to the Charlie Hebdo cartoons was still under investigation, the paper added.
Police said state security had taken over the investigations.
The regional daily, the Hamburger Morgenpost, had splashed three Charlie Hebdo cartoons on its front page after the massacre at the Paris publication, running the headline "This much freedom must be possible!"
Police said the attack occurred at about 1:20 AM GMT (2:20 AM Central European Time) and that two people had been detained, while state security had opened an investigation.
Whether there was a connection between the Charlie Hebdo cartoons and the attack was the "key question", the police spokesman said, adding that it was "too soon" to know for certain.
Police declined to provide further information about the suspects.
Two Islamic jihadists stormed the offices of Charlie Hebdo on Wednesday, killing a total of 12 people including some of France`s best-loved satirists.
Both men were killed Friday in a standoff with police.
Bild am Sonntag newspaper reported earlier Sunday that the bloodshed in France could signal the start of a wave of attacks in Europe, citing communications by Islamic State leaders intercepted by US intelligence.
Shortly after the bloodbath in Paris, the US National Security Agency had intercepted communications in which leaders of the jihadist group announced the next wave of attacks, the tabloid said, citing unnamed sources in the US intelligence services.