German Chancellor Angela Merkel on Monday lamented her party's "painful defeat" in a crucial state poll and blamed the debacle on fears sparked by the Japan nuclear crisis.

She said after a meeting of her Christian Democrats that their loss of power Sunday in their conservative heartland Baden-Wuerttemberg after 58 years at the helm meant that the party could not return to "business as usual".

"That is a watershed moment for the state and also in the history of the Christian Democratic Union. We will have to work through this painful defeat with our friends in Baden-Wuerttemberg for a while to come," she said.

"The debate in connection with the Japanese nuclear plant of Fukushima was clearly what led to our defeat. ... My view of atomic energy has changed since the events in Japan."

Merkel, 56, said she was a supporter of nuclear power but that the post-tsunami crisis at the Fukushima plant had led her to rethink her position.

Declaring Japan's emergency a "turning point", Merkel earlier this month suspended for three months a planned extension of the life of German nuclear reactors, four of which are in Baden-Wuerttemberg.

She also temporarily shut off the country's seven oldest reactors pending a safety review.

Nuclear power is unpopular in Germany, but polls indicated that voters saw Merkel's zigzagging as an electoral ploy; it cost her support while boosting the Greens.

Adding to the pressure, tens of thousands of Germans hit the streets Saturday in four major cities to protest the government's nuclear policy. Organisers said as many as 250,000 took part.

The anti-nuclear Greens doubled their score in Baden-Wuerttemberg and tripled it in the western state of Rhineland-Palatinate, where they are expected to form a coalition with the Social Democrats.

On Monday Merkel ruled out a cabinet reshuffle or an end to her coalition with the embattled pro-business Free Democrats, who failed to win seats in Rhineland-Palatinate and barely scraped in in Baden-Wuerttemberg.

"We had trouble at the beginning, that's perfectly clear, but we have accomplished a lot together and we will continue to do so in the remaining years of this term," she said of her almost 18-month-old centre-right alliance.

She congratulated the Greens on their success but warned that they had to turn what could be seen as an anti-nuclear protest vote into a viable programme.

"The Greens had a very good outcome yesterday. But there's a difference between being in the opposition and bearing responsibilities in the government," she said.