Gregoire Ndahimana, now in his early sixties and mayor of Kivumu district in western Rwanda at the time of the 1994 genocide, had initially been sentenced to 15 years in jail in 2011.
The UN court had found him guilty of failing to take measures against police involved in an April 1994 attack on Tutsis who had taken refuge in the church in Nyange, a parish in Kivumu, and of having "tacitly approved" the destruction of the church the following day.
They also ruled he had acted "as part of a joint criminal enterprise aimed at exterminating the Tutsi in Kivumu district".
The judges said Ndahimana had celebrated the bulldozing of the church by drinking beer with other local officials.
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"The appeals chamber overturns the jail term of 15 years and imposes 25 years in prison," judge Theodor Meron told the court.
When the sentence was read out, the former mayor collapsed into a chair and his wife wept in the public gallery.
Ndahimana was arrested in August 2009 in the east of the Democratic Republic of Congo, to where many Hutu extremists fled after the genocide.
The role of the church in the genocide, in particular the Catholic church, remains controversial.
In the anti-Tutsi pogroms of 1959 and 1962, Tutsis who sought refuge in churches were spared.
Three decades later, during the genocide, they flocked by tens of thousands into churches to escape their executioners. This time round however, they died there massively, hacked to death, burned alive or blown up with grenades.