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Visitors who require a visa for tourism are allowed to visit for up to three months, with the duration of stay decided by the border guards. This appears to be a legal delegation. (Source: Israel Ministry of Foreign Affairs). There is a mechanism for applying for an extension to your stay.
We can assume that entry of non-visa visitors is similarly controlled.
The general principle applied elsewhere is that a visitor should not be attempting to circumvent the requirements of other visas by making repeated visits. Thus, a number of short visits over a limited period is unlikely to be a problem, but repeated visits of 90 days will quickly be shut down.
All of this is dependent on the exact circumstances and the eloquence of the visitor, which is why it's delegated to the border guards.
If you're looking for a rule of thumb, assume you must leave the country for at least as long as your visit.