"It is very disappointing that I am having to withdraw from the Commonwealth Games team," said Sullivan, who won silver in the men's 100m freestyle in the 2008 Beijing Olympics.
"This wasn't an easy decision but it has been made with the longevity of my career in mind, and with Rio as my ultimate goal."
Sullivan was one of the six infamous Australian swimmers who were warned for using the sedative Stilnox and indulging in pranks at their training camp in Manchester before the London Games.
The 28-year-old overcame two shoulder operations to win the national 50m freestyle title from a field featuring James Magnussen to qualify for his third Commonwealth Games team.
"Whilst my shoulder operation went well, and I have done everything in my control to get myself training at the level I know is required to compete at the Commonwealth Games, it is simply not race ready and I do not feel that I will be in a position to compete at my best in Glasgow," Sullivan added.
"In my brief time back on the team, it has been fantastic to see the great sense of team work and re-invigorated camaraderie.
"Australian swimming is heading in the right direction, and I am looking forward to seeing the team do their best in Glasgow."
Swimming Australia performance director Michael Scott lauded Sullivan for his decision.
"Eamon is an experienced athlete who has made a very mature decision with his long term health and fitness in mind, and the goal of competing at a fourth Olympic Games in Rio," Scott said.
(Reporting by Sudipto Ganguly; Editing by John O'Brien)
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