The 48-year-old was captured soon after the attack as he was trying to flee on a bicycle, police said in a statement.
Berlin city police detectives have now taken over the case and are investigating.
Flyers supporting the far-right “German Resistance Movement” (Deutsche Widerstandsbewegung) were found at the Chancellery and at the man's home.
Police said it was the ninth such attack on politically significant buildings since August 2014.
The German Resistance Movement claimed responsibility for a Molotov attack at the fence of Schloss Bellevue, the residence of the German President, in May.
A 50-year-old was arrested after that incident but later released.
Similar attacks were carried out in August against the Christian Democratic Union (CDU) headquarters in Berlin and later on the Reichstag building and the nearby Paul Löbe House, also a part of the central Berlin parliamentary complex, in March and April,.
Far-right perpetrators were suspected in at least one of the attacks.
No-one was hurt in the attack on Thursday, and police did not say how much damage was caused to the Chancellery building.