According to the Daily Telegraph, the condoms were discovered when plumbers were called in to clear the toilets after athletes complained about the blockages.
Condoms, being supplied free at the Games Village, are not biodegradable waste because of which they can choke toilets.
A large condom vending machine has been installed at the village, which contains at least 4000 contraceptive packs.
Officials have said that over half the condoms had already been taken.
Meanwhile, Municipal Corporation of Delhi (MCD) officials said that the civic agency was not responsible for the management of the waste generated inside the Village."We are not dealing with the garbage inside the Games Village towers. We haven't analysed the exact proportion of degradable and non-degradable garbage. It will be done after the Games," MCD's Public Relations officer Deep Mathur said.