The People's Daily said that decision was made despite ambiguous rules. It also criticised a ruling depriving a Chinese cyclist of a gold medal in the women's team sprint and unfounded doping allegations made against swimming sensation Ye Shiwen.
"In ruling on infringements, making accusations of poor sportsmanship and raising suspicions about a genius competitor, there are double standards that have taken aim at the Chinese team and its athletes," said the paper, the main voice of the ruling Communist Party.
"This unfortunately is hard to explain as inadvertent mis-steps, it might be closer to the truth to see it as deliberate attacking and interference."
Last week China was rocked by the expulsion of its top-seeded women's doubles pair Yu Yang and Wang Xiaoli, among eight badminton competitors kicked out for playing to lose group matches with the aim of gaining more favourable draws in the knockout rounds.
Nonetheless, China completed a sweep of all five badminton golds, clinching the men's singles and doubles titles at the London Games on Sunday.
The People's Daily said the furore in the sport had been used unfairly against China.
"Though there can be different understandings of the rules of competition, the Chinese delegation nevertheless voiced its respect for the punishment," said the paper.
"Yet some Western media still seized upon this to deliberately disparage the Chinese athletes and delegation."
The paper noted British cyclist Philip Hindes's sprint team kept their golds, even though the rider was reported as saying he crashed on purpose - words his team later said were "lost in translation"..
"Levelling all the accusations at Chinese athletes plainly lacks fairness," said the People's Daily.
China's basketball hero Yao Ming also waded into the badminton controversy, saying over the weekend the expelled players were victims although he also supported the decision to disqualify them.