Australian PM Julia Gillard has said she is "surprised and disappointed" by Malaysia's treatment of Senator Nick Xenophon and vowed to press for an explanation of his deportation.
Mr Xenophon was detained as he tried to enter on Saturday and returned to Australia on Sunday.
An outspoken critic of human rights in Malaysia, Mr Xenophon was on an election fact-finding mission.
The Malaysian government said he had broken the law during an earlier visit.
But Mr Xenophon said he had been detained because he was considered "a security risk" and that the expulsion order had come from the "highest levels".
Ms Gillard said the Australian government had made "immediate and strenuous representations on his behalf, not only in relation to him being detained, but into him being allowed to be in Malaysia".
She added: "Clearly we didn't succeed in getting the agreement of the Malaysian government for him to remain. I'm glad that he is back safe and well, but we will continue to pursue this issue with the Malaysian government."
Mr Xenophon said on his return: "The only risk I am is to embarrassing the Malaysia government because of my advocacy for clean elections in Malaysia."
The Malaysian government said Mr Xenophon had taken part in an illegal street protest for electoral reform last April.
The senator said he was caught up in anti-government protests in Kuala Lumpur.
A regular visitor to the country, Mr Xenophon had arrived in Kuala Lumpur as part of an unofficial Australian parliamentary fact-finding mission to assess whether forthcoming elections would be free and fair.
The delegation was scheduled to hold talks with several Malaysian parties, including opposition leader Anwar Ibrahim and officials from the election commission.
After Mr Xenophon's detention, the other three members of the Australian team cancelled their trip.
In his blog, Mr Anwar said Prime Minister Najib Razak should not regard visitors as "enemies of the state" simply because they were critical of the ruling party.
Immigration chief Alias Ahmad said in a statement; "Malaysia is a free and democratic country, but no-one is above the law."
Elections must be held by May and Mr Najib's coalition could face a close contest.