Anyone suspected of having a serious contagious disease such as Ebola could face five years in prison if they defy orders to stay at home.
New human biosecurity control orders enable a health department official to force anyone with signs or symptoms of a listed disease to isolate themselves or face arrest.
The director of human biosecurity can also order someone to be vaccinated or treated.
Government legislation setting up the orders, which can be in place for three months, cleared parliament on Wednesday, creating new rules aimed at preventing the spread of disease in both human populations and agriculture.
The government expects the human control orders to be “seldom used” but believes they are important to manage serious communicable diseases, especially in light of the recent Ebola epidemic.
Several people have arrived in Australia from Africa with Ebola symptoms since the disease took hold in 2014, but there have been no confirmed cases.
The legislation allows biosecurity officers to conduct searches without warrants in emergencies related to pests or disease.
The tougher measures were introduced to parliament by Labor in 2012 but lapsed when an election was called in 2013.
The government believes the new laws are vital to maximise Australia’s agricultural productivity and prevent significant damage to the sector. Australia’s agricultural exports were worth $39.4bn in 2013-14.