Angela Merkel has publicly raised concerns over the reported persecution of gay men in Chechnya with Vladimir Putin, following wide-ranging talks.
The German Chancellor raised the alleged capture and torture of more than 100 people at a joint press conference with the Russian President in Sochi.
The Kremlin has backed the Chechen government's denials over the brutal campaign, saying it had "no information" to support research by journalists and human rights groups.
Ms Merkel called on the Russian government to properly investigate the allegations and ensure that LGBT people are fully protected in the territories and elsewhere.
She also called for freedom of assembly to be protected, after Russian riot police arrested protesters demonstrating against the persecution. “It’s important to have the right to demonstrate in a democracy, and the role of NGOs is very importance,” Ms Merkel said.
“I asked Mr Putin to use his influence to protect these minority rights, as well as in the case of Jehovah’s Witnesses.” Russia’s Supreme Court recently banned the Christian sect as an “extremist organisation”, placing it under the same laws as Isis and Nazis.
Ukraine and Syria dominated the pair's meeting, with the German Chancellor calling on Russia to guarantee repeatedly failed ceasefires in both wars.
In Ukraine, Russia supports separatist rebels fighting the EU-backed Kiev government, while it is allied with President Bashar al-Assad in Syria.
Mr Putin claimed his government condemns the use of chemical weapons by any party in the conflict and called for an investigation. "Those guilty must be found and punished, but this can be only done after an impartial investigation," he said.
“A solution in Syria can be only found by peaceful means and under the aegis of the United Nations."
But the Kremlin has repeatedly refuted reports – including from French intelligence services – saying a sarin gas attack that killed dozens of civilians in Khan Sheikhoun was carried out by the regime.
In Ukraine, a peace agreement struck in Minsk has been repeatedly violated by both sides as fighting continues.
Mr Putin claimed the Ukrainian government was the illegitimate product of a "coup" against pro-Russia President Viktor Yanukovych, and blamed Kiev for the separation of two rebel republics.
Ms Merkel said she disagreed with his interpretation of the conflict, where Russia was accused of violating international law by annexing the Crimean peninsula in 2014.
The conflict is one of several issues driving worsening relations with the West, as well as accusations of interference in elections in the US, Germany and elsewhere.
Mr Putin dismissed a journalist’s question on the claims at Tuesday’s press conference, saying accusations of aiding Donald Trump’s campaign were unproven “rumours” used for internal politics.
“We never interfere in other countries’ politics and we want no one to meddle in ours,” the Russian President said. “Unfortunately, we have seen the opposite happening for years. We have seen attempts to influence political processes in Russia through the so-called NGOs and directly.
“Realising the futility of such efforts, it has never occurred to us to interfere. “
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