Bhupathi objected to seedings given to singles specialist players, saying it would keep them safe while some of the good teams will face-off each other in the first round and get eliminated because of the unusual seedings this time.
He said Israeli third seeds Jonathan Erlich and Andy Ram would face France's Arnaud Clement and Michael Llodra in the first round while singles specialists David Ferrer and Nicolas Almagro of Spain, being fifth seeded, will avoid early exit.
"You've got some great doubles teams playing each other in the first round and these singles guys get to play doubles.
I don't think they deserve to be seeded, honestly," Bhupathi said.
"Teams like Ferrer and Almagro might be dangerous teams but they definitely don't deserve to be seeded in the doubles draw," he added.
According to the International Tennis Federation rules, teams can be seeded based on the players' singles or doubles ranking at the Olympics while in other tournaments, only the doubles ranking applies.
"There's got to be some consistency in this world. You can't just show up to the Olympics and do what you feel.
"All these singles guys get to play doubles in the Grand Slam as well but they don't get seeded, so why are they seeded at the Olympics?
"It is the first time I've seen this happen. I don't know what's the agenda with the ITF is, but I think it's pretty unfortunate that they're doing that," Bhupathi added.
Bhupathi (34) also hit out at those doubting India's prospect in tennis because he and Paes (35) were in their mid 30s.
"I think we're still capable of winning matches, unlike what the media says. We do have a chance so let's see how it goes here.
"We're here to win the tournament. It doesn't really matter who we play -- we just have to make sure we're ready on day one," Bhupathi said.