The Israeli official speaking on condition of anonymity said two prisoners were being released as a "goodwill gesture" after the return of the remains of Israeli soldier Zachary Baumel earlier this month.
The decision was not part of a pre-arranged deal, he said.
The official did not provide details on the prisoners but Moscow's envoy for Syria in an interview with Russia's RT television said they were Syrians.
Alexander Lavrentiev said Russia was grateful to Syria for helping to return Baumel's remains, adding that Israel had decided to free a number of Syrians in return.
Israeli soldiers fought against Syrian forces in a battle on June 10-11, 1982 in the Lebanese village of Sultan Yacoub, near the Syrian border.
Some 20 Israeli soldiers were killed in that fighting.
Baumel and two other soldiers, Zvi Feldman and Yehuda Katz, were listed as missing and presumed killed. The latter two remain missing.
The return of the remains of soldiers missing in action is a highly important issue in Israel, which has fought repeated wars with its Arab neighbors since its 1948 founding.
Israeli media reported that the prisoners set to be released were Zidan Tweil and Hamis Ahmed.
Russian President Vladimir Putin said during a visit by Netanyahu that the remains had been found by the Russian and Syrian armies.
Syrian Information Minister Imad Sara on April 4 said that Damascus had no knowledge of plans to repatriate the remains, nor was it aware of the details behind the discovery of the body and its subsequent transfer.