The workers were on a fishing boat when Israeli navy forces detained them and took them to an unknown location, the fisheries directorate within the ministry said in a statement.
The fishermen were identified as Mohammad Ali Sultan, Ismael Ali Sultan and Sami al-Naddi from Rafah.
The statement said incidents of arrests and abuse of Palestinian fishermen has been on the rise recently, and particularly during the fishing season.
The ministry called on the Red Cross to intervene on behalf of the detained fishermen.
An Israeli military spokesman did not immediately return calls.
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