"Of course they are playing together, 100 percent," coach Nandan Bal told Reuters on Thursday.
The 2002 Pusan Games gold medallists have eight doubles grand slam titles between them, but split on the tour a few years ago due to personal differences.
They appeared set for another ugly break up in the Qatari capital after their shock first round defeat to Taiwan in the team event two days ago.
Paes, the team captain, said Bhupathi's fitness was poor after he failed to hold serve once in the straight sets loss.
Indian newspapers reported that Indian tennis officials had to intervene to keep them together in their search for elusive gold medals.
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Indian media also said Paes had initially insisted Bhupathi should take a fitness test.
National selector Akhtar Ali slammed the infighting and criticized coach Bal for openly siding with Paes.
"People are laughing," he told Reuters. "It is not good for the image of Indian tennis.
"An open spat like this while representing one's country is not nice."
In the build-up to the games, Bhupathi initially pulled out after the nation's top woman player Sania Mirza was paired with Paes for the mixed doubles. He was eventually persuaded to come back into the fold.
India won one gold, a silver and two bronze medals at the 2002 Games in Pusan.
(Additional reporting by Sanjay Rajan in Mumbai)