"It is a shocking event that Alexei Navalny has become the victim of an attack with a chemical nerve agent in Russia," said government spokesman Steffen Seibert in a statement.
"The government condemns this attack in the strongest terms. The Russian government is urgently requested to provide clarifications over the incident."
Tests carried out by the German army in consultation with the Charite hospital in Berlin, where Navalny is being treated, had found "unequivocal evidence of a chemical nerve agent from the Novichok family," Seibert said.
Navalny, 44, fell ill after boarding a plane in Siberia last month. He was initially treated in a local hospital before being flown to Berlin for treatment.
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The Charite hospital has reported "some improvement" in Navalny's condition but he nevertheless remains in a medically induced coma and on a ventilator.
The case has drawn parallels with two suspected Kremlin-linked poisonings in Britain.
In 2006, President Vladimir Putin was blamed for the radiation poisoning death of former KGB agent Alexander Litvinenko in the British capital.
In 2018, the Kremlin was also accused of being behind the attempted murder of ex-double agent Sergei Skripal in Salisbury, southwest England, using a Novichok nerve agent.
The German government said it would inform NATO and EU partners over its findings and seek a joint reaction on the case.
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