The Russian president was in France for talks with Macron, two weeks after his election victory. Macron's call comes after widespread reports of a brutal campaign by the authorities against gay men in Chechnya, including allegations of torture and murder.
"I emphasized to President Putin...how important it is for France to respect all people, all minorities," Macron said during a news conference with the Russian leader.
"We spoke about the cases of LGBT people in Chechnya... I told President Putin what France is expecting regarding this issue, and we agreed to regularly check on this subject."
Macron added that President Putin told him he had started a number of initiatives with regard to the Chechen LGBT community. Previously, Putin said he would talk to the prosecutor general and interior minister regarding an investigation.
The French president has added his voice to that of German Chancellor Angela Merkel
who, also during a recent meeting with Putin, asked the Russian president to guarantee the rights of minorities in Chechnya.
Before the meeting, protesters stood in front of the Eiffel Tower with a banner which read "Stop homophobia in Chechnya."
The allegations of abuse in the mainly Muslim republic of Chechnya have drawn international condemnation after the claims were first reported in a Russian newspaper in April
Beatings and Electrocution
Speaking to CNN on condition of anonymity one man said hundreds of gay men like him had been held in detention centers because of their perceived sexual orientation.
"They started beating me with their fists and feet. They wanted to get names of my gay friends from me," another Chechen man told CNN at a safe house.
"Then they tied wires to my hands and put metal clippers on my ears to electrocute me. They've got special equipment, which is very powerful. When they shock you, you jump high above the ground."
Many of the men are now in hiding after escaping Chechnya. Although the Russian government has said it will look into the claims, activists say they are now working on getting the victims out of Russia.
Tatiana Vinnichenko from the Russian LGBT Network says the organization is discussing visas with four European countries. The Lithuanian foreign minister, Linas Linkevicius, says visas have already been issued to two gay men from Chechnya who were "persecuted because of their sexual orientation."
Although some countries have welcomed the men, Vinnichenko alleges others, such as the United States, have been unresponsive to requests for help.
"We tried to start a dialogue and ask for visas with the American embassy [in Moscow] and they refused us," Vinnichenko told CNN.
"The United States will not give visas," she said.
The US State Department told CNN it was unable to discuss individual visa cases but "continues to be concerned about the situation in the Republic of Chechnya.'"
The US ambassador to the United Nations, Nikki Haley, had previously condemned the abuse, calling on the Chechen authorities to "hold anyone involved accountable, and take steps to prevent future abuses."
Vinnichenko has shared with CNN new graphic images of abuse allegedly inflicted on a gay man in Chechnya. The image was shared with the victim's permission.
In one picture, severe bruising is clearly visible on a man's buttocks and legs.
"This was done in a prison for gay people," Vinnichenko said. "People are afraid to go to the police, to say a crime has been committed. The message from...Russia is, "nothing is happening, they are inventing it all,'" she said.
Human Rights Watch says
men targeted by the anti-gay purge in Chechnya are not safe in Russia. Vinnichenko agrees.
"Their lives are in danger. These people could be killed," she told CNN.
"When they were handed back by the police to their relatives in Chechnya, they were 'outed.' The police told the relatives, 'You know what you have to do.' They encouraged the relatives to kill their own flesh and blood," Vinnichenko said.
In Chechnya, homosexuality is considered by many to be shameful. So-called "honor killings" - murder by family members to atone for disgrace - are a real threat.
The Chechen authorities have denied accusations by human rights groups and media reports of the abuse.
"There is not a single piece of evidence to prove that such people exist in Chechnya, let alone are subject to persecution," the Chechen Human Rights Ombudsman, Nurdi Nukhazhiyev, said.