SYDNEY, Mar 25 (Reuters) Australia is braced for its most serious disruption of relations with Indonesia since bloodshed over East Timor independence in 1999, after Jakarta recalled its ambassador from Canberra over Papuan asylum seekers.

Ambassador Hamzah Thayeb flew out of Canberra yesterday night over what the Indonesian government described as Canberra's ''deplorable'' decision to grant temporary protection visas to 42 West Papuan asylum-seekers.

This is the first time Indonesia has recalled an ambassador to Australia in protest and reactions in Australia today mostly dismissed efforts by Australian Foreign Minister Alexander Downer to play the matter down.

''If we don't manage this issue very carefully ... it will do a lot of damage to our relationship,'' Hugh White, Professor of Strategic Studies at the Australian National University, told Australian Broadcasting Corp radio.

Potential damage would increase if Australian public opinion in support of West Papuan breakaways grew strongly to pressure the Australian government into a more accommodating approach to West Papuan independence sentiment, he said.

Australian Greens Senator Bob Brown on Saturday called on the Australian government to take up the issue of West Papua in the United Nations.

About 1,000 students in hiding in Papua were ''terrorised by the Indonesian troops'', he said.

Indonesian affairs expert Harold Crouch, also of the Australian National University, said the Indonesian government's reaction was understandable.

''They (Australia) are taking a particularly strong line,'' he told Reuters.

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