In a statement published on Tuesday they also showed understanding for the protests against the treaty.
"It is with regret that we realise that this outrage has a just cause," it said. The church's handling of sexualised violence has not always met the high standards that society rightly expects of it. However, the protection of the confessional secret must be separated from this: "It is not a privilege of the church or the confessor. It only concerns the act of the sacrament of reconciliation and protects the penitent, not the priest."
Any questioning of the secrecy of confession would above all harm the religious freedom of the faithful, the bishops emphasised.
The agreement regulates the legal status and fields of activity of the Catholic Church in the Czech Republic in 16 articles. This includes the Church's right to maintain educational and charitable institutions. It also regulates pastoral care in prisons, social institutions and hospitals as well as in the police and armed forces.
The explicit protection of the seal of confession is controversial among the Czech public. Critics of the treaty fear that it favours the covering up of abuse. In their declaration, the bishops emphasise that they are committed to ensuring that the church is a safe place where no one has to fear violations of dignity through sexualised violence.
This also includes the criminal prosecution of offences and cooperation with law enforcement authorities.
The treaty is the result of years of negotiations.
In 2003, a first attempt to conclude a treaty with the Vatican failed due to a parliamentary veto.
The aim of the treaty is to continue to guarantee the religious freedom of the faithful and consequently also the freedom of the Church to fulfil its mission, the Vatican announced immediately after the signing.
In October, Cardinal Secretary of State Pietro Parolin and Prime Minister Petr Fiala signed the basic Treaty between the Holy See and the Czech Republic in Prague in October.
The Czech Senate approved the agreement at the end of January and the treaty will be on the agenda of the Chamber of Deputies in March. The basic treaty can only enter into force once both chambers have approved it.
Opponents of the treaty have announced that they will take legal action against ratification after a motion in the Senate to have the treaty reviewed by the Constitutional Court prior to approval failed.
The agreement would put the relationship between the state and the Catholic Church in the Czech Republic on a contractual basis for the first time.