But Putin, speaking in Moscow on Tuesday, rejected that Israel was to blame for the "friendly fire" incident as both Russian Federation and Israel raced to defuse tensions and prevent a major flare-up of tensions in southern Syria where both air forces operate.
A United States official with knowledge of the incident said Monday that the Syrians were trying to stop a barrage of Israeli missiles when the Russian aircraft was hit.
In an attempt to strike back against the Israelis, the Syrians launched extensive anti-aircraft fire, the official said and the Russian aircraft was hit.
Putin and Israeli Prime Minister Benjamin Netanyahu were scheduled to speak by phone later yesterday, Israel's Channel 10 television reported.
Israel's military expressed "sorrow" on Tuesday for the deaths of crew members of a Russian military aircraft accidentally downed by Syria during an Israeli strike, but blamed Syrian President Bashar al-Assad and Iran.
A witness in Latakia told Reuters that he spotted four missiles downed by Syrian air defences. However, it could not confirm their identity and Syria has made no official comment.
"Using the Russian jet as a shield, the Israeli pilots put it in the fire of Syrian air defense systems", Russian media quoted Defense Ministry spokesman Major General Igor Konashenkov as saying.
The Russian plane was "not within the area of the operation" carried out by the Israeli jets, it said.
An Israeli military official recently said it had hit more than 200 Iranian targets in Syria over the past 18 months, with Russian Federation largely turning a blind eye, a situation Israel would want to continue.More news: China, Russia begin joint military drills
So far nothing indicates Russian military bases have been targeted, but Syria-based correspondents have reported Russian air defences operating.
Syria's coastal city of Latakia, which hosts a large Russian naval base and military presence, has come under attack from an unclaimed missile strike that Syria attributes to Israel. This absolutely does not correspond to the spirit of Russian-Israeli partnership. "As a result of the irresponsible actions of the Israeli military, 15 Russian service personnel perished".
Israel rarely acknowledges carrying out specific airstrikes in Syria, but is believed to be behind dozens of attacks on Iranian forces and Hezbollah weapons shipments.
"I offer condolences first and foremost to the relatives of those killed", Putin said.
Mr Putin said Moscow's response would aim at securing the safety of Russian military personnel in Syria's complex civil war in which various outside powers have backed opposing sides.
Putin said the two leaders agreed to create a 15-20 kilometre-wide demilitarised zone along the line of contact between rebels and regime troops by October 15.
There was no comment from Israel on the incident.
Russia's defense minister rejected the Israeli assessment.