In November 2003, Cotan took up a post as Ambassador of Indonesia to Australia. Speaking about on his time in Australia at the end of the posting in 2005, Cotan reflected that the relationship was difficult when he first came to Canberra in 2003 because of events that happened in East Timor in 1999. Cotan said the aid and relief Australia's military had provided to Indonesia in the wake of the 2004 Indian Ocean earthquake and tsunami had brought the two countries closer. He said however that he was stunned at the way Australians reacted to the arrest and sentencing of Schapelle Corby for drug smuggling in 2004–05—some Australians wanted the country's tsunami aid taken into account in Corby's sentencing.