The Club's president Sultan Ahmed, who is also the Union Minister of state for Tourism, claimed they have the evidence and they would lodge a complaint with the game's governing body and also write to AFC and FIFA.
The Sikkim outfit owned by Indian icon and retired footballer Bhaichung Bhutia, who also plays for his team rode on a penalty to draw Mohammadan Sporting 1-1, that enabled them make the I-League topping second division standings.
Ahmed said the Sikkim outfit was awarded unfair penalties in all the matches.
"It was a clear case of biased refereeing. In every match, they have taken advantage of penalties. We have the footage," he claimed.
"We will lodge a formal complaint with the AIFF. We would even write this to the sports ministry, the AFC and FIFA. Let them know, how the football is being run in India," the Union MoS said.
Mohammadan Sporting coach Aloke Mukherjee alleged that Sikkim outfit even took the help of police to threaten them.
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"After they were awarded a penalty, we protested the decisions. But the police officials intervened and threatened to arrest us. They even lathicharged. We were helpless. There was not even a single AIFF representative for such a crucial match," Mukherjee said.
"We had beaten them (2-0) in Siliguri in the first-leg and yesterday also we were dominating the proceedings."
He also criticised the idea of staging the championship in two legs -- Silguri and the final leg in Gangtok, something that gave the home side an unfair advantage.
AIFF secretary Kushal Das said they would surely look into it if a formal complaint was lodged.