India has already asked the Australian government to curb the anti-India activities.
The Honorary Consulate of India in Australia's Brisbane city was targeted by Khalistani supporters who raised the Khalistan flag at the office, the latest in a series of radical activities against the Indian community in the country, according to a media report on Friday.
The incident came days after External Affairs Minister S Jaishankar visited the country and emphasised the need for vigilance against "radical activities" targeting the Indian community in Australia.
According to The Australia Today portal, the Honorary Consulate of India located on Swann Road in the Taringa suburb of Brisbane was targeted by Khalistan supporters on the night of February 21.
Honorary Consul of India in Brisbane Archana Singh found the Khalistan flag attached to the office when she arrived on February 22, the report said.
Ms Singh immediately notified the Queensland Police, which on arrival confiscated the flag and swept the Honorary Consulate of India to clear of any immediate threat.
"Police are surveilling the area to keep us safe. We have Strong faith in police authority," Ms Singh told The Australia Today.
The incident comes following the vandalism of three Hindu temples in Australia by Khalistani supporters.
On January 23, the management of the International Society for Krishna Consciousness (ISKCON) temple also known as the Hare Krishna Temple in Melbourne's Albert Park found the walls of the revered temple vandalised with graffiti "Hindustan Murdabad".
On January 16, the historic Shri Shiva Vishnu Temple in Carrum Downs, Victoria, was vandalised in a similar manner.
On January 12, the Swaminarayan temple in Melbourne was defaced by 'anti-social elements' with anti-India graffiti.
Mr Jaishankar and his deputy V Muraleedharan during their visit on February 18 to Sydney and Melbourne respectively have raised India's concerns over the issue.
Mr Jaishankar during his meeting with his Australian counterpart Penny Wong discussed the issue.
"Noted the forward movement on our bilateral agenda. Emphasised the need for vigilance against radical activities targeting the Indian community," Mr Jaishankar tweeted after the meeting.
However, on the same day, Khalistani supporters threatened two Hindu Temples while they were celebrating Mahashivratri, the report said.
India has already asked the Australian government to curb the anti-India activities of the Khalistani separatists and also attacks on the Hindu temples in the country.
"Signals that pro-Khalistan elements are stepping up their activities in Australia, actively aided and abetted by members of proscribed terrorist organisations such as the Sikhs for Justice (SFJ) and other inimical agencies from outside Australia, have been evident for some time," the Indian High Commission in Canberra said in a strongly-worded statement on January 26.
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