Russia blamed Israel for the crash, saying the plane was caught in the crossfire as four Israeli fighters attacked targets in northwestern Syria.
Russia said that Israel warned it of the impending strike just one minute beforehand and deliberately created a “dangerous situation.”
Russian Defence Minister Sergei Shoigu spoke to his Israeli counterpart, Avigdor Lieberman, and told him Moscow holds Israel wholly to blame for the shooting down of the Russian plane, Russian news agencies reported.
In keeping with protocol, Israel has neither confirmed nor denied the allegations that it was behind the attack.
The Russian military said the Il-20 reconnaissance aircraft was hit 35 kilometers (22 miles) off the coast as it was returning to its home base nearby.
Israel's ambassador in Moscow was summoned to the Russian Foreign Ministry over the incident, foreign ministry spokeswoman Maria Zakharova said.
"The Israeli pilots were using the Russian aircraft as a shield and pushed it into the line of fire of the Syrian defense," ministry spokesman Maj. Gen. Igor Konashenkov said in a statement.
Russia said it would make an "appropriate response" to Israel.
"We view the actions of the Israeli military as hostile," Konashenkov told Russian state television. "As a result of the irresponsible actions of the Israeli military, 15 Russian service personnel perished."
He said the Israeli pilots "could not have failed to see the Russian aircraft, as it was coming in to land from a height of 5 km (three miles). Nevertheless, they deliberately carried out this provocation."
"This absolutely does not correspond to the spirit of Russian-Israeli partnership," the spokesman said.
"We reserve the right to take commensurate measures in response," Konashenkov added, without giving details of what those measures would be.
Dmitry Peskov, spokesman for President Vladimir Putin, told reporters that the Kremlin is "analyzing the situation" and does not want to speak further at this point.
The Kremlin emphasized that Israel's short notice did not give the Russian plane enough time to escape.
A recovery operation in the Mediterranean Sea is underway, Konashenkov said.
However, Syria and Russia were quick to attribute the strike on the coastal city to the Israel Air Force.
According to the Russian news agency Sputnik, the strike was intended to hit a warehouse storing drones and missiles.
The Lebanese Al Mayadeen news channel, the main site attacked was the Technological Industries Corporation.
Al Jazeera said that the missiles were fired from the sea, while CNN reported that according to TASS, the ministry of defense specified that "the mark of IL-20 went off the radars disappeared during the attack of four Israeli F-16 aircraft on Syrian targets in the province of Latakia."
Arabic Sky News quoted sources claiming that the missiles hit a base housing Iranian militias.
The Syrian Center for Monitoring Human Rights reported Tuesday that two people were killed in the attack.
Russia's defense ministry said early on Tuesday that one if its military aircraft with 14 people on board disappeared from radar screens over Syria at the same time that Israeli and French forces were mounting aerial attacks on targets in Syria.
A US official said Washington believed the aircraft, which is an Il-20 turbo-prop plane used for electronic reconnaissance, was inadvertently shot down by anti-aircraft artillery operated by Moscow's ally, the Syrian government.
For several years, Israel and Russia have maintained a special hotline to prevent their air forces from clashing in the skies over Syria. Israeli military officials have previously praised its effectiveness.
Russia has been a key backer of Syrian President Bashar Assad and it has two military bases in the country, including one close to the Mediterranean coast.
Sima Shine, a former senior Mossad official and ex-deputy director-general at the Strategic Affairs Ministry, told Israel's Army Radio station that the shooting down is problematic both militarily and internally from a Russian perspective.
Israel has refrained from taking sides in the Syrian civil war. But it has acknowledged carrying out scores of airstrikes against archenemy Iran and its Shi'ite proxy Hezbollah.
Israel has also acknowledged attacking Iranian targets some 200 times. Israel has warned that it will not allow Iran to establish a permanent military presence in postwar Syria.
"I think it will impose very serious restriction on Israel's freedom of activity," she said.
Reuters, Associated Press and Ynet contributed to this report.