The Russian Il-20 warplane with 15 people on board was shot down by the Syrian air defence late Monday.
The plane downed by Syria's Russian-made S-200 air defence had a crew of 15, who were all killed, Moscow said.
The downing was reported to have occurred about 35km from the Syrian coast as the Il-20 aircraft was returning to Russia's Hmeimim airbase near Latakia.
An Israeli diplomatic source said Israeli Prime Minister Benjamin Netanyahu was expected to speak shortly with Putin.
According to a handout from the Russian Ministry of Defense of a conversation between Israeli Defense Minister Avigdor Liberman and his Russian counterpart, Army General Sergei Shoigu, Shoigu described the actions of the Israeli air force as irresponsible and said to Liberman that the fault for the downed plane and the deaths of its crew "rests entirely with the Israeli side".
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There was no immediate word from Damascus, but the deadly air war sequence started when missiles struck the coastal region of Latakia on Monday.
Syrian officials have so far not commented.
Russian Federation has a peace treaty with Israel, but it is also using its military to prop up the regime of Syrian dictator Bashar al-Assad.
RIA reports the Russian ministry accused Israeli pilots of putting the Russian aircraft in the path of Syrian missiles. "We reserve the right to take appropriate action in response".
A row between Israel and Russian Federation could restrict Israel's ability to mount air strikes inside Syria on what it considers the greatest threat to its security from the Syria conflict: build-ups of Iranian forces or groupings of the Iranian-backed Hezbollah militia.
Russian Federation has blamed Israel after one of its reconnaissance aircraft carrying 15 people was shot down by a Syrian surface-to-air missile over the Mediterranean Sea.
The command of Russia's air base at Khmeimim launched a search and rescue operation.
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According to Konashenkov, the Israelis had given Russian Federation "less than one-minute" warning before the 10 pm strike on Latakia province, where Russian Federation has a base.
Putin did not voice his grievances against Israel but said he supported the Defence Ministry's statement. "It will be something everyone will notice", Putin said.
The statement also laid blame on Iran and the Lebanese Shia militant group, Hezbollah, two other allies of the Syrian government.
"This is absolutely not in keeping with the spirit of the Russian-Israeli partnership".
The Israeli and Russian militaries maintain what they call a "deconfliction mechanism", which is meant to coordinate their activities in Syria in order to avoid incidents like this one.
Russia's defense minister rejected the Israeli assessment.
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