Judges did not agree with power plant operators that the shutdown ordered by lawmakers in 2011 amounted to an "expropriation" of their assets, but said the government should agree a deal to compensate the firms by June 2018.
"It was permissible for lawmakers to take the accident in Fukushima as a prompt to speed up exiting nuclear energy to protect the health of people and the environment," senior judge Ferdinand Kirchhof told the court in Karlsruhe.
The judges did not specify how much the compensation should be, but media reports said the plaintiffs -- German electricity giants EON and RWE and Sweden's Vattenfall -- had sought some 20 billion euros (USD 21 billion) in damages.
Merkel's government decided after Japan's 2011 Fukushima reactor meltdowns to halt operations of Germany's eight oldest nuclear plants and to shutter the other nine by 2022.
The move marked a sharp reversal for Merkel, who had earlier overturned a phase-out ordered by a previous government in 2002.
"We cannot simply accept that parliament disregarded constitutional requirements by providing for no compensation," he said at the time.
"For our shareholders -- including many small stock holders who have their savings and pensions invested with us -- this creates a significant financial loss which under current law will not be compensated for."
The firms have complained that the losses come at a time when they are already struggling in the face of low wholesale electricity prices and competition from heavily subsidised renewables as part of Germany's shift to clean energy such as wind, solar and biomass.
At the same court hearing in March, Environment Minister Barbara Hendricks defended the government's position, saying that the Fukushima catastrophe had "necessitated a reassessment of the risks associated with nuclear energy".
The verdict could have an impact on parallel negotiations between the government and nuclear plant operators on managing the country's atomic waste disposal.
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