Sports Minister Maken told reporters here that he has informed the MEA on the issue.
"I have already informed MEA about the matter and I am waiting what they want me to do," Maken said here.
The visa denial had created a friction between the MEA and the Sports Ministry with the former maintaining that it should have been kept in the loop.
"Sports Ministry should have consulted the MEA before going ahead with such a tour to avoid any such incident," official sources said.
The Sports Ministry, on the other hand, insisted that the visa denial to the delegate came at such a late stage that nothing could have been done.
"We were informed about this visa denial at a very late stage. We were told just moments before the flight was to take off. It was not possible to do anything at that stage," a Sports Ministry source said.
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Chinese authorities denied the visa to the Arunachal Pradesh delegate earlier this week but the 100-strong Indian delegation still went ahead with the tour.
The delegation is in Beijing on the invitation of the All China Youth Federation as part of the program under the scheme of "the Year of China-India Friendship and Cooperation", jointly announced by Chinese President Hu Jintao and Indian Prime Minister Manmohan Singh.
This is not the first instance of China refusing visa to residents of Arunachal, which Beijing calls its own territory. Such incidents of visa refusal have happened in the past concerning government officials and sportspersons, including shooters, weightlifters and a karate team from the state.