The Ivorian international said he was the victim of racist abuse from the stands during his side's 2-1 Champions League victory at CSKA Moscow on Wednesday at the Khimki Arena on Moscow's outskirts.
The claim could be embarrassing for President Vladimir Putin, who is struggling to contain ethnic tension in Russia as it prepares to host he 2014 Winter Olympics in February and the 2018 soccer World Cup.
While British newspapers condemned the chants, Russian media were mostly silent and CSKA played down the incident.
"We didn't hear any shouts from the stands that Toure spoke of," CSKA director general Roman Babayev said, according to state-run news agency Itar-Tass.
"Moreover, there were various remarks and noises sounded from the stands, aimed not only at black players," he was quoted as saying on Wednesday night. He could not be contacted again on Thursday.
He also suggested Russian fans were not racist, saying: "There are Africans at CSKA, too: Ahmed Musa, Seydou Doumbia. And they have never encountered such problems."
Despite that claim, there have been at least six incidents of reported racism involving Russian clubs in the last five years.
Former Brazil defender Roberto Carlos was greeted with racist banners and had bananas thrown at him playing for Anzhi Makhachkala against Zenit St Petersburg and Krylia Sovetov Samaria in March 2011.
In March 2012 Lokomotiv Moscow fans threw bananas at Anzhi defender Christopher Samba while last December a supporters group from Zenit demanded in a statement that the club should not sign any black players.
Toure, one of the most respected figures in the game and who learnt Russian while playing for Metalurg Donetsk in Ukraine for three years, reported the racist chants to Romanian referee Ovidiu Hategan 10 minutes after halftime.
However, Babayev, while promising that CSKA would "closely examine" the issue, added: "I think he jumped to conclusions.
"My understanding is that he spoke of an episode in the 85th minute when he and Edin Dzeko fell near the penalty area."
Babayev continued: "It's possible that our fans tried to put pressure on the Manchester City players at that moment. But it is premature to say these efforts were racist."
CSKA coach Leonid Slutsky said he did not hear any racist chants either, according to Itar-Tass.
"I was focused on the match," he said.
Toure's anger comes at a time when ethnic tension is higher than usual in Moscow.
The stabbing death of an ethnic Russian man was widely blamed on a migrant from mostly Muslim Azerbaijan, touching off a nationalist riot on Oct. 13 - the biggest outbreak of ethnic unrest in the capital in three years.
Putin underlined Kremlin concerns that ethnic or religious tensions could threaten Russia's unity in comments on Tuesday.
He accused foreign rivals of using radical Islam to weaken Russia and deflected any responsibility for ethnic and religious strife, putting the blame partly on local authorities.
In December 2010, several thousand youths rioted just outside the Kremlin, clashing with police and attacking passersby who they took for non-Russians after the killing of an ethnic Russian soccer fan was blamed on a man from the North Caucasus.
A spokeswoman for the Russian Sports Ministry declined to comment and referred questions to the minister, Vitaly Mutko, who could not immediately be reached.
The Russian Soccer Union also declined to comment while European soccer's governing body UEFA, who declared this week Football Against Racism in Europe Action Week, made a cursory statement saying that were waiting for the match officials' report before making any further statement.