Kim Jeong-Wook -- captured in the North last October -- faced an array of charges including illegally entering the country, spying for Seoul's intelligence agency, running an underground church and other "anti-state propaganda and agitation", according to the North's official KCNA news agency.
He admitted all the charges before being sentenced to hard labour for life, the agency said yesterday.
The trial was held after Pyongyang ignored repeated pleas by Kim's family and his lawyer from Seoul to meet him, the South's unification ministry said today.
"We would like to say clearly that the latest action not only violates international customs but also humanitarian spirit which is universal for all humankind," it said in a statement.
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The ministry also urged Pyongyang to "show a responsible stance" by responding to months-long calls by Seoul and the international community to free Kim.
Fellow activists and missionaries said Kim had been providing shelter and food for seven years to North Korean refugees living in China's northeastern border city of Dandong.
Although religious freedom is enshrined in the North's constitution, it does not exist in practice. Religious activity is restricted to groups linked to the government.
Pyongyang views foreign missionaries as seditious elements intent on fomenting unrest.
A number of missionaries -- mostly US citizens -- have been arrested in the isolated communist state in the past. Some were allowed to return home after interventions by high-profile US figures.
Kim's sentence came at a time of high tension between the two Koreas, which have in recent months traded fire across their tense sea border.