Indonesia says it wants the right to verify any serious claims made by Papuan asylum seekers.
A spokesman for the embassy in Canberra says his government appreciates the prime minister John Howard's rejection of Papuan independence.
But the spokesman, Dino Kusnadi, says Indonesia is still unhappy Australia gave temporary visas to 42 West Papuan boat people.
The West Papuans claimed they needed protection because of persecution by the Indonesian military.
In the latest protest by Indonesia, the country's Importers' Association has now called on its members to boycott Australian products.