Peres will have a private audience with Benedict XVI on Thursday.
At the end of Monday's four-hour meeting, the two delegations released a joint communiqué, reporting that they "carried forward their work in an atmosphere of cordiality."
The delegates are focused on negotiating the "comprehensive agreement," which deals with relations between the Church and Israel regarding issues of taxation on material goods and ecclesial property.
The agreement, set out in the Fundamental Agreement signed in 1993 by the Holy See and Israel, has yet to be fully agreed upon.
It is hoped that Peres' visit to the Holy See will speed up negotiations, since he drew up the Fundamental Agreement while serving as Israeli minister for foreign affairs.
The next set of meetings between the Holy See and Israeli delegations will take place Nov. 7.
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