He said the invitation to the Dalai Lama had gone before the Tibet agitation started.
However, the Chief Minister said he was afraid the External Affairs Ministry may not give permission to the Dalai Lama to visit Tawang.
Ruling Congress and opposition BJP differ on whether the Dalai Lama should be be allowed after the unrest in Tibet.
BJP Lok Sabha member from Arunachal (West) Kiren Rijiju, also a Buddhist, said the Dalai Lama is basically a spiritual leader and the Indian government should not impose any ban on his entry in Tawang for inaugurating a hospital.
The importance of the Dalai Lama's possible visit to Tawang could be assessed from the fact the spiritual leader, after the failed uprising against the Chinese, had taken the Tawang route to flee to India in 1959. Secondly, in the 1962 war, the Chinese army had captured Tawang and came up to Bomdila. The red army later withdrew.
However, Rijiju, who is the coordinator of All Party Parliamentary Forum for Tibet, agrees with the chief minister's stand that predominently Monpa Buddhist communities should not be allowed to come out on the streets of Tawang or ny other part of the border state in support of Tibetans.
Arunachal Pradesh is passing through a difficult period and none should be allowed to aggravate the situation, he said.
Khandu said he has advised the local people to pray for the Tibetans inside the 400-year old monastery, the second largest in Asia after Lhasa, housing 500 lamas.
The autorities have promulgated prohibitory orders under section 144 Crpc.
The BJP MP said people in other parts of the country should, however, openly agitate in support of the Tibetans as India was directly affected by the influx of Tibetans and he will lead agitations of Tibetans when the olympic torch arrives in New Delhi on April 17.
China has been claiming Arunachal Pradesh, including Tawang, the birth place of the 6th Dalai Lama, as its territory but India rejected the claim and asserted the state was an integral part of its territory.