The former England international believes Roy Hodgson has made a mistake by leaving the defender at home and thinks that his ex-team-mate's international career is now over
The Three Lions boss has been victim to criticism after overlooking the former national-team captain despite the recent injury to defender Gary Cahill.
And former England striker Fowler had dismissed Hodgson's statement that the 33 year-old has been omitted for 'football reasons.'
"There's not a chance Rio Ferdinand was left out of the England squad for 'footballing reasons'. Not a chance. The public knows that too," Fowler wrote on his Paddypower.com blog.
Current England defender John Terry has an impending court case hanging over him for alleged racist comments to Rio's brother Anton during a Premier League game between QPR and Chelsea last season.
Fowler considers this situation as the reason why Ferdinand will not be taking part in Poland and Ukraine.
"The reason is Rio's brother, Anton, was allegedly racially abused by John Terry," he added.
"I've read that Ferdinand got in touch with Hodgson shortly after he was appointed as manager to say he was willing to play in the same England team as Terry."
Fowler, a former team-mate of Ferdinand, is convinced that the defender should've been included in the 23-man squad but fears his international career may now be over.
"I played with Rio Ferdinand at Leeds United. He is a fantastic player who reads the game brilliantly. He started 30 Premier League games for Manchester United last season and nearly won the league. Footballing reasons?
"Rio is a quieter defender than John Terry. Terry is more dominant, and yes, England need that. Roy Hodgson doesn't want to concede goals. I would still have taken Ferdinand.
"But this looks like the end of his England career, to be honest."
Meanwhile, the Football Association confirmed that on Tuesday the entire England squad "took part in some form of recovery work or training" ,but failed to elaborate on the fitness of certain players.
Chelsea defender John Terry suffered a tight hamstring in England’s friendly over Belgium on Saturday and was due to have further tests.
There have been fitness concerns over other players in the past fortnight but the FA is yet to confirm any fresh injury concerns.