"There are in Nigeria two advisers who have dealt in terrorist matters in the past," he told AFP. "They were sent there by the state to help."
The pair were not currently serving as intelligence personnel for the Israeli government.
"They are not soldiers, not officers. They are not part of the security system," the source added.
On May 11, Israeli Prime Minister Benjamin Netanyahu called Nigerian President Goodluck Jonathan with an offer to help search for more than 200 schoolgirls kidnapped by Boko Haram.
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Jonathan accepted immediately.
"President Jonathan welcomed the offer by Mr Netanyahu to send a team of Israeli counter-terrorism experts to assist in the ongoing search and rescue operations," the Nigerian leader's office said.
Specialist teams from the United States, Britain, and France have been sent to help in the search operation, which Nigeria's military has said is concentrated on the Sambisa forest area of Borno state.
Boko Haram, whose name is loosely translated as "Western education is forbidden", kidnapped the girls from their dormitory on April 14, and has threatened to sell them.