Steffen Seibert said it was a "big political and social task" to phase out nuclear energy but was worthwhile - and reaped new technological and industrial benefits.
In the immediate wake of the 2011 disaster at Japan's Fukushima nuclear plant, Germany decided to shutter its nuclear reactors by 2022 and ramp up the use of renewable power sources.
Japan announced its plan to phase out nuclear power by 2040 on Friday, apparently bowing to public pressure after last year's disaster, the worst atomic accident in a generation.
"You can imagine that Germany, which has now had some experience of the path towards the future of renewable energy, willingly stands with all Japanese institutions with help in both word and action," Seibert told reporters, before underlining that Tokyo had only just made its decision.
"The Japanese know what we too know - that they have posed themselves a very big political and social task," he said.
"It's worth it for the nation that goes down this path. It creates new technological possibilities, it creates new industry export potential, but it is definitely a very demanding task, as we can say from experience, he added.
Seibert also said he could see broad scope for Germany and Japan swapping advice and expertise.
Japan's move also brings it into line with Italy and Switzerland.
The German government has come in for criticism for what industry officials say is a cripplingly slow approach to its energy transition programme.