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Clergy have been taken off the government payroll and will no longer be paid as civil servants.
Although they will still be paid by a state subsidy fund, Tuesday's decision marks a significant shift in the status of bishops, and the separation of Church and state in Greece.
This deal was made and announced by Prime Alexis Tsipras and the head of the Church of Greece, Archbishop Ieronymos.
Prime Minister Tsipras said: "I would like, if you allow me, to begin by saying that this meeting is the culmination of a dialogue that has begun a long time ago, both between us, but also between the State and the Church."
He said that the aim of these decisions was to deal with historic disagreements that hinder current functioning and to make the church self-reliant.
He said: "It solves many decades of outstanding issues that have arisen since the 1920s, but mainly because it is an Agreement for the benefit of both sides" and used language of "mutual respect".
The main change was that: "The Greek State undertakes to pay annually to the Church in the form of a subsidy an amount corresponding to the current salary cost of the active priests, which will be adjusted according to the salary changes of the Greek State."
The move takes over 9000 church staff off the payroll and onto a separate state fund, not necessarily altering their pay but ending their direct salaries from the state. However, an increase in the number of clergy would not require the fund to increase.
The fund will be managed by a five-member board. Two members of the Fund will be appointed by the Church of Greece, two members appointed by the Greek Government and one member appointed jointly.
The Church, in return, will not be allowed to oppose moves to make the country religiously neutral - an intention of Syriza, the left-wing party which is in power.
It must also drop claims to properties which both the Church and State have fought over in the past.
Despite these steps, the country remains deeply religious in the traditional sense, with clergy present in the swearing-in of new governments and the recognition of the Greek Orthodox Church in the constitution.
A representative of the clerics' union, Father Georgios Vamvakidis told a Greek radio station that most bishops opposed the agreement and that Archbishop Ieronymos did not have the authority to sign it on their behalf.
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