Foreign ministry spokeswoman Johanna Westlund told AFP the Russian ambassador, Viktor Tatarintsev, was summoned due to "alarming reports that homosexuals in Chechnya have been imprisoned and tortured".
Tatarintsev met state secretary Annika Söder, who "emphasized that the Russian government has a responsibility to make sure that human rights are respected on all of Russia's territory", Westlund said.
She would not disclose the Russian's comments, saying only: "He confirmed that he would pass on the message to Moscow."
The Kremlin said Thursday that reports of violence against homosexuals in Chechnya had not been confirmed and that "phantom complaints" to the media should instead be taken to the police.
The comments come a day after Russian President Vladimir Putin met Chechen strongman Ramzan Kadyrov, who dismissed "provocative articles" about gay men being rounded up in Chechnya and families who are encouraged to perform honour killings.
Russia's prosecutor general said last Monday that it was looking into the claims.
AFP has spoken to several Chechens currently in hiding in Moscow after fleeing the conservative Caucasus region where homosexuality is taboo and authorities have said that gays do not exist.
The men said they were beaten and detained in unofficial prisons, and had fled the region because they were terrified of both the authorities and their own relatives.