Dr McNaughton died at his home on Christmas Eve.
He was a leading campaigner for East Timorese rights and brought the atrocities being inflicted on them by the Indonesian army and militias to the attention of the world.
East Timor's foreign-affairs minister, Jose Ramos Horta, says Dr McNaughton made an important contribution to his country's independence.
Jefferson Lee, from the Australia East Timor Association, says Dr McNaughton campaigned tirelessly for the East Timorese' right to self-determination.
"Andrew was inspiring at every level. He was a relentless campaigner against hyprocrisy and humbug from the politicians and foreign-affairs bureacrats both here in Australia. He was probably the most influential person in the Labor Party changing its position in 1998-1999 from one of accepting East Timor's incorporation to once again supporting self-determination."
After East Timor gained independence, Dr McNaughton did not stop.
He continued campaigning to ensure Australia gave East Timor a greater share in the oil and gas fields that lie in the sea between the two countries.
Mr Lee says Dr McNaughton had become a great personal friend of many of East Timor's senior politicians and is revered by many East Timorese.
"Every Timorese person that I've ever met speaks nothing but highly of Dr Andrew McNaughton. They are aware of his role in supporting the liberation of his country, none more so than its leaders."
Mr Ramos Horta will be among the country's leaders attending the funeral.