PRAGUE — Churches were seized, priests jailed or even executed and those allowed to lead religious services did so under the watchful eye of the secret police. More than 22 years after the fall of Communism, the Czech government agreed Wednesday to pay billions of dollars in compensation for property seized by the former totalitarian regime.

The deal at one point, however, threatened to topple the coalition government after a junior partner this week voiced anger at the thought of huge sums being paid to churches given the current economic gloom.