The rules on exports of drugs, biologics and medical devices from the United States (which are summarized here) are sufficiently complex that it is understandable that Israeli Customs might not understand them completely. However, since Levaquin is an approved drug in the United States, it can be exported with FDA approval (at least as long as it is being exported for an approved use).

Probably Israeli Customs was referring to an FDA export certificate. The FDA export certificate program is described here. Basically an export certificate is a document that is not mandatory for export but which may be requested by the importing country as a guarantee that the pharmaceutical meets the quality standards of the exporting country.

(For the conspiracy-minded, Levaquin is in the same class of antibiotics as Cipro and is an approved treatment for inhalational anthrax. It is also approved for other types of bacterial infections as well.)