Churchill Brothers have alleged foul play by match officials and demanded replay of their Federation Cup football semi-final with Mahindra United.
The Goa side lost 1-4 to Mahindra United on Wednesday in the semi-final after being the first team to score.
In a letter to All India Football Federation secretary Alberto Colaco, Churchill Brothers' patron Churchill Alemao took strong exception to the casual approach of the referee, especially under television glare. His grouse was the Surkumar Singh's equaliser which came in unfortunate circumstances.
"The referee should have stopped play when N S Manju was down on the ground and awarded a foul in favour of Churchill Bros for contact with the goalkeeper," Alemao wrote in the letter.
"Knowing the gravity of head injuries, all our players appealed for the ball to be put out and desisted from active play. The referee didn't bother to protect the injured player," he added.
Alemao also complained that assistant referee Cham Suklama failed to flag Jose Ramirez Baretto off side while scoring Mahindra's second goal.
It effectively killed off the match and Churchill Brothers' prospects in the tournament, the letter said.
Insisting that casual approach of the referees was an insult to Churchill's contribution to football, he demanded a replay of the semi-final.
The AIFF, however, is unlikely to treat the letter as a protest since it was lodged 21 hours after the game.
According to article 16 of AIFF's Federation Cup rules, "protests if any shall be lodged in writing with the match commissioner within two hours after the end of the match".
The protest should also be accompanied by a protest fee of Rs 5,000.
The letter was submitted at 6.30 pm on Thursday evening.
The protest letter, without the fee, was addressed to AIFF general secretary and not to the match commissioner.
AIFF general secretary Alberto Colaco said the matter has now been referred to the match commissioner.
"The match commissioner is the competent authority to decide on technical matters," Colaco said.