New biosecurity measures mean Australians suspected of having contagious diseases could be arrested for failing to comply with stay-at-home orders.

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 a suite of 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, however there have been no confirmed cases.

The legislation also 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 agriculture productivity and prevent significant damage to the sector.

Australian agricultural exports were worth $39.4 billion in 2013-14.