Clarence House ended the confusion Monday by issuing a statement, Press Trust of India reported.
A diplomatic incident had loomed over whether Charles or Indian President Pratibha Patil should preside over Sunday's opening ceremony in New Delhi, The Guardian reported.
For the first time in 44 years, Queen Elizabeth II will not attend the games. Indian officials were said to balk at giving the honor to the prince in the absence of his mother, the head of the commonwealth.
India had been pushing for the president to open the event as national pride has been badly dented by criticism of local organizers.
After weeks of scandals, star pullouts and criticism over the state of the athletes' accommodations at the Games' village, organizers were relieved as traditional powerhouses such as Australia and Canada and a second batch of English athletes checked in Monday. The village was described as "uninhabitable" by Commonwealth Games Federation officials last week.
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