Mrs Merkel's Christian Democrats had met with its junior partners on Sunday after the ethics panel had delivered its conclusions.
Before the meeting she said: "I think we're on a good path but very, very many questions have to be considered.
"If you want to exit something, you also have to prove how the change will work and how we can enter into a durable and sustainable energy provision."
The Fukushima plant was crippled by the March earthquake and tsunami in Japan, causing radioactive leaks that spurred anti-nuclear protests in Germany.
Mr Rottgen said a tax on spent fuel rods, expected to raise 2.3bn euros ($3.28bn) a year from this year, would remain despite the shutdown.
Germany's nuclear industry has argued that an early shutdown would be hugely damaging to the country's industrial base.
Before March's moratorium on the older power plants, Germany relied on nuclear power for 23% of its energy.
The anti-nuclear drive boosted Germany's Green party, which took control of the Christian Democrat stronghold of Baden-Wuerttemberg, in late March.
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