Green Party leader and Environment Minister Ville Niinisto told reporters Thursday that the decision clashes with the core values of the anti-nuclear Greens, a junior partner in governing coalition since 2011.
The exit weakens Prime Minister Alexander Stubb's coalition though it retains a majority in Parliament by one seat.
Earlier Thursday the government extended a license to Finnish-Russian consortium Fennovoima to build a nuclear reactor in Pyhajoki, northern Finland. Initially granted in 2010, the license was set to expire next year.
It would be Finland's sixth reactor. The four reactors currently in operation provide about 25 percent of Finland's electricity needs. Another one is under construction.