Acting on a tip-off, soldiers searched the church and discovered material and accessories for making suicide kits of the type generally used by the LTTE, the ministry said.
There was no immediate comment from the church.
Separately, the military also uncovered eight sticks of dynamite, detonators and steel balls hidden in sand in the central district of Kandy, the ministry said.
It also accused the LTTE of gunning down a Sinhalese university student late Thursday in eastern Batticaloa district.
Tens of thousands have died on both sides since the rebels began fighting in 1972 for an independent homeland for minority Tamils on the majority Sinhalese island.
The latest deaths raised to 6,020 the number of rebels that the government says have been killed since January. The ministry says 562 soldiers have died during the same period.
Colombo has scrapped a truce and poured a record 1.
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5 billion dollars into this year's war effort in what it says is an all-out b