"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."
The regional tabloid 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!"
No one was hurt in the attack, which police said occurred at about 0120 local time.
Two people were detained, while state security has opened an investigation, police said.
Whether there was a connection between the Charlie Hebdo cartoons and the attack was the "key question", the police spokesperson said, adding that it was "too soon" to know for certain.
Police declined to provide further information about the suspects.
No one at the Hamburger Morgenpost, known locally as the Mopo and which has a circulation of around 91,000, could immediately be reached for comment.
"Thick smoke is still hanging in the air, the police are looking for clues," the newspaper said in its online edition.
Media reports said the newspaper's publishers had ordered private security protection for the building in the western district of Othmarschen.
German news agency DPA reported that the attack had occurred from a courtyard of the building and hit the newspaper's archive room where some records were destroyed.
It quoted a police spokeswoman as saying that the editorial team should be able to continue work in the building as the damage was relatively minor.
Two extremists 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.
Several German newspapers had published the Charlie Hebdo cartoons on their front pages Thursday in a gesture of solidarity with the French cartoonists and in defence of free speech.
Germany's 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 militant group announced the next wave of attacks, the tabloid said, citing unnamed sources in the US intelligence services.
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The world stands united against 1000-year old ideologies. The unbelievable 3-million strong march in Paris showed that the world has moved on. The line has been drawn in the sand. Any disrupting force will be dealt with in the only way possible.
It is important that the so called freedom of speech is revisited because it is nothing more than an all out assault on Islam by the extremists in the Christian West.
Muslims must remember that there is no power on earth that can destroy let alone insult a religion. It is the people of that religion who alone have the power to do so and Muslims are fulfilling that role splendidly. Furthermore Muslims must remember to counteract the satirisation they must assimmilate well and live cooperatively with the society where they have made their homes. In France suburbs and towns where Muslims are in majority a non-Muslim French person is afraid to go even the police are scared because of violence. Such behaviour should be stopped if Muslims are to leave there.
Muslims didn't get jobs even before the attacks. Now, even the low-paying jobs will not be available.
US new war dog in making.. ISIS