Hockey coach Jose Brasa was also not invited for the ceremony held Friday.
Fernandez, who has tirelessly worked with the Indian boxers for more than a decade, said he is as much a part of the team as other coaches and wanted to be part of the momentous occasion.
"It would have been an honour to meet the PM. I am with the team for so long. I wanted to be there with the team. We did so well in the Games. But they said only one coach is allowed. So, I did not have much option but to back out," Fenandez told IANS.
India's Chief coach G.S. Sandhu was present with the team during the ceremony. India won three gold and four bronze medals in boxing during the Oct 3-14 Games.
The Cuban said he is happy that the boxers are getting the due recognition for their consistent performances but the coaching staff, who spend hours with them during training, also deserve to be awarded more often.
"We are there with the boxers all the time. It is great to see boxing getting popular in this country but one must not forget the efforts put in by coaches like me in training of these boxers," said Fernandez.
On India's chances in the upcoming Asian Games in China, Fernandez said the competition will be a lot tougher than what the Indian pugilists faced in Delhi but is confident of at least two medals in the sport.
"You have countries like Kazakhstan and Uzbekistan which have world class boxers. Chinese are also a force to reckon with in the lighter weight categories. Getting medals will be a lot tougher there," he said.