A number of witnesses and victims gave CNN horrific accounts of torture, saying that hundreds of gay men were being rounded up by authorities and held in appalling conditions in least three detention centers.
"We've heard some very negative reports about how homosexuals are treated in Chechnya, and I asked Mr. Putin to use his influence to ensure the rights of such minorities," Merkel told reporters after meeting with Putin in the Russian city of Sochi.
Chechnya is one of several semi-autonomous republics within Russia.
Being gay is considered by many in the Muslim-majority republic to be shameful, and in Chechnya the practice of so-called honor killings -- murder by family members to expunge shame -- is widespread.
In April a Chechen government spokesman called the allegations of a crackdown "an absolute lie," and denied that gay men exist in the republic.
Putin: US election meddling 'nothing but rumors'
Merkel also stressed the importance of civil rights to Putin, including the right to demonstrate and the right for NGOs to operate freely.
Russia has passed a series of laws in recent years that has made protesting nearly impossible and has clamped down on NGOs that voice opposition to the Kremlin or that receive foreign funding.
Putin was also asked by a reporter for his response to a spate of attacks on Russian opposition figures in recent weeks. Putin's main political opponent, Alexey Navalny, was reportedly hit in an acid attack this week, as were several other activists.
Putin responded by saying that law enforcement agencies were working within the law and that victims had access to the justice system.
"The law enforcement agencies in Russia are acting in a much more mitigated way than many of our partners in Western Europe."
He also shot down allegations of Russian interference in the US and European elections.
There have been concerns of Russian meddling in upcoming European polls
, including the French vote on Sunday and Germany's election in September.
"We never interfere in the political processes of other countries, and we would very much appreciate it if no one interfered in our political life. Unfortunately, for many years we have seen the opposite: Influence on political processes in Russia, through so-called non-governmental organizations and directly," he said in response to a reporter's questions, without giving specific examples.
"You referred to the example of the United States, which has not been confirmed by anyone and is nothing but rumors used in a domestic political struggle in the United States."
Ukraine and sanctions
The leaders did not speak explicitly about sanctions at the press conference after their meeting, but they both said they were committed to the Minsk agreements
aimed at bringing an end to the Ukraine crisis, despite slow progress.
Merkel has openly backed the European Union's decision to place sanctions on Russia following Moscow's annexation of the Crimean Peninsula from Ukraine in 2014. She has been the lead mediator in talks with Russia over Crimea.
The agreements involve a ceasefire, and pulling weapons and pro-Russian forces out of the area. They were brokered by Merkel and French President Francois Hollade.
The EU sanctions -- as well as US sanctions -- on Russia have been a thorn in the Kremlin's side. Moscow has lobbied world leaders to drop the restrictions that have taken a toll on the country's economy, already sluggish on low oil prices.
Gernot Erler, Germany's top Russia policy official, said earlier that Merkel would reiterate Berlin's position that sanctions against Russia could be lifted swiftly if Moscow adhered to the Minsk agreements, according to the Berliner Zeitung newspaper.
Merkel conceded that the political process had been slow, but brushed off suggestions by reporters that it should be scrapped and replaced with a new instrument.
"Our objective is that Ukraine will get access to its own border, but before that, a ceasefire then a political solution should be found," she said.
"We need implementation and (some) sides need to step up."
Merkel and Putin split on Syria
The two leaders also discussed the Middle East -- their governments stand on opposing sides of the Syrian war. Putin is the most powerful ally of embattled Syrian President Bashar al-Assad, while Merkel has openly called for Assad's ouster.
Erler, the German official, acknowledged earlier that a peace deal for Syria was no longer possible without Russia, which he described as "the savior of Assad."
He suggested that Merkel might push Putin to allow other foreign countries to take part in future negotiations.
Russia is currently holding ceasefire talks with warring factions in Syria's war. It is working only with Turkey and Iran on the deal.
"We have to acknowledge that all previous peace efforts have failed. The UN Special Envoy, Staffan de Mistura, has not made any progress. But also the ceasefire talks initiated by Russia have not led to any tangible results," Erler told Berliner Zeitung.
Merkel's trip comes as Berlin-Moscow relations remain stuck at a low over the Ukraine crisis and Syrian war. But the visit to Russia -- Merkel's first in two years -- appears to mark a thaw in relations.
Putin and Merkel, both stalwart leaders in their countries, have kept regular communications open over the years. Both speak each other's language and have overseen periods of expanded Russian-German trade relations.
But that closeness didn't come immediately. Putin was infamously accused of trying to intimidate Merkel in her early years as Chancellor, when he brought his dog -- a large black Labrador named Koni -- into a bilateral meeting and press conference in 2007.