John Short, 75, was picked up at Beijing airport by an Australian embassy vehicle and would only say he was feeling very tired.
He was accused by Pyongyang of committing a crime by distributing tracts from the bible at a Buddhist temple in Pyongyang on Kim Jong Il's birthday, a national holiday in North Korea to mark the ruling dynasty's second leader.
In his "confession", Mr Short said: "I deeply apologise for what I have done by spreading my Bible tracts on February 16th - the birthday of his excellency Kim Jong Il.
"I realise the mass media of the USA and the western countries who say that the DPRK is the closed country and has no religious freedoms is inaccurate and wrong."
North Korea said that it had decided to deport Mr Short partly because of his age.
Mr Short's wife Karen endorsed her husband's Christian mission, saying she would not change anything despite his jailing in Pyongyang.
She said: "He's done what he's done because that's what he believed."
Pyongyang has held American missionary Kenneth Bae for more than a year and convicted him of trying to overthrow the state.