"China has no business telling us what to do and what not to do (regarding the Dalai Lama's movement). It is not our next-door neighbour. India shares boundary with Tibet, not with China," he told reporters in Bomdila.
"In reality, the McMahon Line demarcates the boundary between India and Tibet," he said.
Mr Khandu, who accompanied the Dalai Lama during an eight-hour-long drive from Guwahati to Bomdila on Tuesday, said it was a brave decision on the part of the Tibetan spiritual leader to undertake the arduous trip.
"He wanted to reach Tawang anyhow and the weather could not deter him. Let us hope that his followers here get satisfaction from his discourses," he said.
This is the Dalai Lama's sixth visit to Arunachal Pradesh as a state guest since 1983 and he has been to Tawang every time except in December 1996.
His last visit in 2009 was planned exactly 50 years after he had crossed through Arunachal Pradesh, then North East Frontier Agency, after escaping from Lhasa.
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