John Short was picked up at Beijing airport by an Australian embassy vehicle and did not speak. (Agencies)
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.
"I deeply apologise for what I have done by spreading my Bible tracts on February 16th the birthday of his excellency Kim Jong Il," Short said in the confession released by KCNA and dated March 1.
Short admitted wrongdoing and apologized, KCNA said, and released photos that showed him authoring a three-page handwritten confession and using red ink to mark each page with his thumbprint.
"I realise that 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," Short said in the confession, which was written in English using language consistent with North Korean propaganda.
North Korea, officially known as the Democratic People's Republic of Korea (DPRK), said it had decided to deport 75-year-old Short partly in consideration of his age.
Short's wife Karen endorsed her husband's Christian mission, saying that she would not change anything despite his jailing in Pyongyang.
"He's done what he's done because that's what he believed to do, other people it's their own life and choice, we're all free to choose," she told Reuters Television in Hong Kong.
Pyongyang has held American missionary Kenneth Bae for more than a year and convicted him of trying to overthrow the state.
While North Korea espouses freedom of religion it is ranked as one of the world's most oppressive regimes in that regard.
A United Nations report issued last month identified a lack of religious freedom in a state whose human rights abuses it likened to those of Nazi Germany.
In a rare media conference last week, a South Korean missionary held in North Korea confessed to spying in the North at the behest of the South Korean intelligence agency and attempting to build an underground church in the country.
John Short was picked up at Beijing airport by an Australian embassy vehicle and did not speak.