The result left supporters angry, and Conlan accused boxing's governing body, the AIBA, of corruption from "the core right to the top". In an emotional outburst during a live television interview, the world-class sportsman said he had been "robbed" of his Olympic dream.
The boxer now intends to follow his brother, Jamie, into the professional ranks.
The AIBA hit back at Conlan's claims, describing them as without foundation. A spokesman said: "Michael is a current world champion and he came here with high expectations.
"His disappointment is massive, we can all understand that. It's his personal judgment.
"AIBA is striving for a fair, level-playing field. The idea is not to benefit one country towards another.
"These statements are groundless, but he's free to have his opinion."
Fellow Belfast boxer Paddy Barnes - who lost a similarly close decision in his first fight - described the AIBA as a "disgrace to sport".
His father, Patrick Barnes, last night made explosive claims that the Russian boxing camp knew Conlan was going to lose to Nikitin before the fight took place. He said: "We knew coming here this morning. The Russians told us that Michael wasn't going to get the contest. They told us that themselves. And we knew."
He went on the describe the defeat as the "ultimate robbery".
Paddy Graham, secretary and coach at Clonard Boxing Club - where Conlan is a member - said he was "disgusted" at the result. "It's blatantly obvious that he won - it's bribery, it's just bribery," he said.
"Michael is disgusted and told it like it is. He's world number one, so he knows what's going on in the background, as he hears things.
"He's coming home the same hero as he went out to us. He was robbed blind.
"When he became the world amateur champion, he was no doubt offered all sorts of money to turn professional.
"He's been training for this for a long time. He will never go back to the Olympics after this, why would he?
"The Russian was cut in the face and eye. I'm surprised he could fight. I am sickened by it."
Twitter also erupted in fury, with many slamming the fight as a "sham". One fan said: "Corruption is rife. The whole thing is a shambles."
However, the Olympic Council of Ireland (OCI) said: "While we understand and share Michael's disappointment with the decision today, the OCI does not condone his comments or conduct. We will evaluate internally before taking any action."
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