The Immigration Minister Scott Morrison has announced his department was cancelling temporary visas for people who had planned to visit Australia from the West African nations and said new visa applications would not be processed.
Permanent visa holders yet to arrive in Australia must undergo a 21-day quarantine process before departure.
Scott Morrison told parliament: "The government's systems and processes are working to protect Australians."
But Sierra Leone's Information Minister Alpha Kanu described the move as "too draconian", insisting that measures put in place at Sierra Leone's Freetown airport had successfully prevented anyone flying out of the country with Ebola.
"It is discriminatory in that... it is not [going] after Ebola but rather it is... [going] against the 24 million citizens of Sierra Leone, Liberia and Guinea. Certainly, it is not the right way to go," he told Reuters news agency. "This measure by the Australian government is absolutely counterproductive."
Amnesty International has also criticised Australia saying the country is taking a "narrow approach."
The United Nations Secretary General, Ban Ki-moon says the travel restrictions will work against the efforts to curtail Ebola.
