The Department of Foreign Affairs and Trade said its focus on the 20-year anniversary was honouring the lives of the victims and the courage and resilience of survivors and their families.
It stressed the Australian government was not involved in organising the event in Bali.
"We are deeply disappointed by the decisions made by organisers. We will be formally registering our concerns with the Indonesian authorities," a department spokesperson said.
"We understand the distress it has caused and stand ready to offer assistance to any Australians who may need it."
Hundreds of Australians and Indonesians packed the foreground of Kuta's ground zero monument for various events to mark the anniversary.
It was the later ceremony timed to coincide with the time of the deadly 2002 explosions just after 11pm that provoked most interest and drew a bevy of high-profile Australian and Indonesian politicians, diplomats, other officials and police to hammer home the fight against terrorism.
In a high-powered security operation, a swarm of elite Brimob, or Mobile Brigade Corps, police and military forces lined the area and shut off streets leading to the ground zero monument.
High-ranking officials attended along with Australian Federal Police officers.
Militant-turned-police informant and deradicalisation proponent Nasir Abbas, who trained the Bali bombers in making explosives, mingled in the crowd.
And a graphic film screened beside the monument, depicting the nightclub explosions and their gruesome aftermath, caused serious distress.
The bombings carried out by Islamic terrorists - the worst in Indonesian history - tore through the Sari Club and Paddy's Bar, killing 202 people, among them 88 Australians on October 12, 2002.
Among survivors at the ceremony were Balinese burns victims Yayuk and Cusnol, each of whom had spent months in emergency care in Perth attended by respected plastic surgeon Fiona Wood.
Both women had suffered burns to about 70 per cent of their bodies.
