City's captain Yaya Toure pointed out to the referee what he claimed was racist chanting from CSKA Moscow fans during the Champions League game, but the referee did not follow UEFA's protocol following such an allegation.
UEFA have already opened disciplinary proceedings against the Russian club for the alleged racist incident.
"UEFA president Michel Platini has requested that the UEFA administration immediately conduct an internal investigation to understand why the three-step protocol established to deal with incidents of a racist nature was not implemented," UEFA said in a statement on Friday.
Referees are empowered to stop matches and ask for a public address announcement to be made urging spectators to stop such racist behaviour, and warn that the game will be suspended and subsequently abandoned if that behaviour continues.
Any decision to abandon the fixture can only be taken after all other possible measures have been exhausted.
Although Toure, an Ivory Coast international, alerted the referee about the incident 10 minutes into the second half, the game, and the chanting continued without the referee taking any action.
CSKA Moscow officials denied there was any racist behaviour or chanting at the game, but the incident has provoked a storm of complaints with Toure on Friday calling for black players to boycott the 2018 World Cup in Russia if racism continues in the country.
Toure called on world governing body FIFA and the Russian government to act, saying "It is very important. Otherwise we are not confident coming to the World Cup in Russia. We don't come."
The focus however now switches to Hategan, a 33-year-old FIFA referee who has officiated at four Champions League matches and 44 matches under UEFA's jurisdiction.
His back up team of assistant referees Cristian Nica and Octavian Sovre, the fourth official Sebastian Gheorghe are Romanian as were the additional assistants Cristian Balaj and Istvan Kovacs - the men who stand behind the goallines in Europa League and Champions League matches.
The UEFA match delegate was Norwegian Tormod Larsen.
UEFA said it will publish the findings of the internal investigation once the disciplinary case has been dealt with by UEFA's independent Control and Disciplinary Body on October 30.
(Reporting by Mike Collett, editing by Pritha Sarkar)
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