According to an army spokeswoman no one was hurt and the troops did not shoot back in a bid to avoid escalation.
"There was shooting from Syria towards an Israeli force south of the Syrian city of Quneitra," an army spokeswoman said about Monday's alleged incident on the occupied Golan Heights.
"The Israel Defence Forces did not respond in order to maintain restraint. A protest was lodged with the United Nations force," she said. UN forces are in the Golan Heights as a peace-keeping force.
Israeli media reports said the soldiers were repairing a border fence when they came under fire from a Syrian army position.
Violence is extremely rare on the Golan Heights, captured by Israel in the 1967 Middle East war.
The United Nations Disengagement Observer Force on the strategic plateau supervises an Israeli-Syrian ceasefire reached after the 1973 Middle East war.