The cause of death wasn't immediately known.
Coates worked for the Bombers from 2000 to '04 before becoming the CFL's director of football operations. He held that post until 2007.
During his time with the league, Coates established its instant replay program, developed a digital video exchange infrastructure and implemented a cardio-vascular screening program for players and coaches. He also created the CFL's code of conduct, dress code and sideline policies.
"Shawn's passion for Canadian football ran as deep as you will find," CFL president/chief operating officer Michael Copeland said in a statement. "He brought energy, enthusiasm and a winning smile to those around him.
"The league has lost a great friend, and he will be missed."
Coates was well respected in football circles for his professionalism on the field and infectious sense of humour and pleasant demeanour off it.
A native of B.C., Coates worked initially as a sports journalist, which brought him to Manitoba in the 1980s. And although he went to Toronto to work at the CFL head office, Winnipeg remained home for Coates.
He returned there following his CFL tenure to become the director of marketing and communications at the University of Winnipeg.
Former rush end Daved Benefield, a 13-year CFL veteran who spent the '02-'03 seasons in Winnipeg, tweeted his condolences after learning of Coates' death. Benefield also posted a picture of the two posing together.
"My friend Shawn Coates has died suddenly," Benefield said on his Twitter account. "Football will miss a man, of his ilk. RIP big daddy, RIP. #CFL #Bombers."
In February 2014, Coates was named the executive director of Football Manitoba after serving as the chief operating officer for Novusoft Solutions, a company that made smartphone apps.
Coates was also an avid sports photographer, his work appearing in such publications as USA Today, the Winnipeg Sun, La Presse and the Toronto Sun.
Funeral arrangements are pending.