The move is considered highly controversial in the Czech Republic, and the left-wing opposition has asked the country's highest legal authority, the Constitutional Court, to stop it.
After the signing, Prime Minister Petr Necas called the deals to pay 59 billion koruna ($3.1 billion) in financial compensation over the next 30 years "an act of justice."
The payment is part of a religious restitution plan approved by Parliament last year. Under it, the 16 religious groups—including Catholics, Protestants and Jews—also will get back 56 percent of their former property now held by the state—valued at 75 billion koruna ($3.9 billion).
The Catholic Church will receive most of the money and property in the deal, which also includes a provision that the state will gradually stop covering priests' salaries and other church expenses over the next 17 years.
Necas said Friday the compensation plan has "laid new, modern ground" for the relations between the state and religious groups.
The story harks back to 1948, when the Communists seized power in what was then Czechoslovakia, a mostly Christian country. The Communists confiscated all the property owned by churches and persecuted many priests. Churches were allowed to function only under the totalitarian state's strict control, and priests' salaries were paid by the state.
At least 65 Catholic priests, monks and nuns were executed or killed in prisons, while others were driven to suicide by the harsh conditions, historians say.
Many religious groups were persecuted across eastern Europe under communist regimes, but the Czech Republic was the last country in the former Soviet bloc to deal with the religious restitution, the government said.
After the 1989 Velvet Revolution brought in democracy, some churches, monasteries and synagogues were returned, but the churches have since sought to get back other assets such as farms, woodlands and buildings.
The opposition Social Democrats said earlier this month that the financial compensation does not appear to be in line with the Constitution because it is unclear how the government reached the 59 billion koruna ($3.1 billion) compensation total. The party also said some of the properties used by the churches in the past didn't belong to them.
It is not clear when the Constitutional Court will issue its verdict.
The Social Democrats' opposition appears to reflect public opinion in a country with one of Europe's highest concentrations of atheists.
Necas dismissed the complaints Friday, calling the deal "a compromise" that was reached through a "maximally transparent" process.