FIFA would not confirm a report in Britain's Mail on Sunday newspaper that the 23 members of Russia's squad at the 2014 World Cup were among those being investigated.
It said that the entire squad underwent pre-competition and post-match doping tests, which were all negative and which were under FIFA's direct control.
Russia's deputy prime minister Vitaly Mutko, who is also head of the Russian Football Union, dismissed the allegations and said there never was nor will be doping in Russian soccer.
"Don't pay attention to this, they have been writing about us negatively since 2010," he told the TASS news agency.
"Our national team is endlessly checked. We have doping tests at all matches. In soccer this has never been a central theme."
A report by Canadian sports lawyer Richard McLaren in December said more than 1,000 Russian athletes competing in summer, winter and paralympic sport were involved in or benefited from an institutional conspiracy to conceal positive doping tests.
The report, commissioned by the World Anti-Doping Agency (WADA) said that more than 30 sports, including soccer, were involved.
Russia will host next year's World Cup and is currently staging the Confederations Cup, considered a dress rehearsal for the 2018 tournament.
"FIFA has simply confirmed that, in close collaboration with WADA, it is still investigating the allegations involving football players in the so-called McLaren report," said FIFA in an emailed statement to Reuters.
FIFA said it had not referred to any particular players and "cannot comment on the status of ongoing investigations." It said it wanted investigations to be completed quickly and that it could not provide further details until then.
"All players participating in the 2014 FIFA World Cup – including all members of the Russian squad – underwent pre-competition and post-match tests, all of which resulted negative," it added.
"FIFA was in charge of the tests and sent all samples to be analysed by the WADA-accredited laboratory in Lausanne."
Russia were knocked out in the group stage of the tournament after losing to Belgium and drawing against South Korea and Algeria.
(Reporting by Brian Homewood in Berne and Moscow newsroom; Editing by Toby Davis)
