The programme has attracted criticism in the past
Producers gave tapes of the show to the police after a female contestant seemed to be held down by one man while another rubbed his crotch in her face.
No charges were made but two men have been thrown off the programme.
"Here is a great opportunity for a bit of self-regulation and get this stupid programme off the air," said Mr Howard.
"It is just a question of good taste," Howard told Australian radio as he condemned the show, broadcast by Network Ten.
Federal Communications Minister Helen Coonan has referred the programme to Australia's television standards watchdog.
But Network Ten issued a statement reaffirming its commitment to the programme.
"Big Brother adheres to all broadcasting codes of practice and all relevant rules and regulations," it said.
The programme's producers said two housemates had been pulled from the show because they broke the programme's rules of conduct.
No footage of the incident which led to their eviction was shown on the TV programme, although it was broadcast live on the internet.
Police said no further action would be taken and the woman involved had not made an official complaint.
The format has been a hit for broadcasters around the world since it made its debut in the Netherlands in 1999.
Producers of India's Big Brother have said that an upcoming celebrity edition will have a ban on "hanky-panky".

A spokeswoman for Endemol India told BBC News that contestants will have to remain chaste in the Big Brother house for three months. "Participants will be told to keep their hands to themselves," she revealed. "India is a conservative society and it is not ready for the raunchy scenes that so characterise the programmes in the West," she added. 

And unlike other versions of Big Brother around the world, India's version will not be transmitted live in a bid to avoid showing unpleasant scenes which may cause controversy. 

It is understood that up to twelve contestants will participate in the show, which is to be televised at the end of this year. The show’s producers have said they want stars from Bollywood, Indian television and cricket to live in the Big Brother compound. The managing director of Endemol India, Rajesh Kamat, said both Hindus and Muslims may be chosen, but that issues between religions would not be talked about on the programme. 

India is still quite a conservative society. Close acts like kissing are never seen on TV, and only a small number of couples cohabit before marriage.

In 2006, two housemates were removed from Australia's version of Big Brother after apparently sexually assaulting a female contestant. 

Big Brother was created in the Netherlands in 1999 and has sold to almost seventy different countries.