Deputy Foreign Minister Sergei Ryabkov said the missiles were a “stabilising factor” that could dissuade “some hotheads” from entering the conflict.
Russia also criticised an EU decision not to renew an arms embargo on Syria.
Meanwhile, the BBC has heard evidence that 200 people were killed in a massacre in western Syria this month.
Opposition activists said they had documented the civilian deaths in al-Bayda and Baniyas after government troops and militias entered the towns.
While the lifting of the EU arms embargo is theoretically good news for the fractious Syrian opposition, it is clearly going to be some time before it has any effect on the battlefield balance. Its authors hope the decision itself will send a strong enough signal to the Assad regime that it is time to hand over power.
That is extremely unlikely. It is hard facts on the ground that count, for a regime that has shown every sign of determination to fight to the end to stay in power. While European arms supplies remain for the moment theoretical, the step has stirred an angry reaction – possibly even an escalation – from the Russians.
They’ve said the move has jeopardised efforts to convene a peace conference, and that they plan to honour a prior contract to supply Syria with advanced S-300 air defence missiles. Israel sees that as a threat to its own security, and has warned that it “would know what to do.”
As the Syrian conflict deepens, the stakes are clearly getting higher by the day. But for the rebels at least the eventual possibility of carefully-controlled arms deliveries is there, in what looks like being a bloody, long-haul struggle.
‘We know what to do’
Mr Ryabkov said the contract for the S-300 missile systems had been signed several years ago.
“We consider these supplies a stabilising factor and believe such steps will deter some hotheads from considering scenarios that would turn the conflict international with the involvement of outside forces,” he was quoted as telling journalists.
Russia’s envoy to Nato, Aleksandr Grushko, said Moscow was acting “fully within the framework of international law”, in delivering the arms.
“We are not doing anything that could change the situation in Syria,” he said. “The arms that we supply are defensive weapons.”
The BBC’s Jim Muir in Beirut says the Russian statement could be seen as an escalation. He says there had been reports that Moscow was holding back on delivering the arms, in exchange for an Israeli commitment not to carry out further air raids over Syria.
Israeli Defence Minister Moshe Yaalon said the Russian missile systems had not yet left Russia.
“I hope they will not leave, and if, God forbid, they reach Syria, we will know what to do,” he said.
Russia has repeatedly blocked efforts to put more pressure on Syrian President Bashar al-Assad.
Along with the US, it has been leading efforts to organise an international peace conference on Syria next month.
The Syrian opposition has not said whether to attend the conference, and was locked in talks in Istanbul, Turkey, as an unofficial deadline to decide on its attendance passed.
On Monday, the EU said member states would be able to decide their own policy on sending arms to Syria, after foreign ministers were unable to reach the unanimous decision required to extend the current arms embargo past Saturday.
However, in a declaration announced after 12 hours of talks, it agreed not to “proceed at this stage with the delivery” of equipment.
The EU’s Foreign Affairs Council is to review this position before 1 August, in light of fresh developments to end the conflict including the ongoing US-Russia peace initiative.
The EU embargo, first imposed in May 2011, applies to the rebels as much as the Syrian government.
Britain and France had been pressing for the ability to send weapons to what they call moderate opponents of President Assad, saying it would push Damascus towards a political solution to the two-year conflict.
Syria’s Russian-made military
- Nearly 5,000 tanks; 2,500 infantry fighting vehicles; 2,500 self-propelled or towed artillery units
- 325 Tactical aircraft; 143 helicopters
- Nearly 2,000 air defence pieces
- 295,000 active personnel; 314,000 reserve personnel
Other EU states had opposed sending arms.
A spokesman for UK Prime Minister David Cameron said the decision sent an unambiguous message to President Assad.
“We are sending a signal loud and clear to the regime and being very clear about the flexibility we have if the regime refuses to negotiate,” he said.
George Jabboure Netto, a spokesman for the opposition Syrian National Council said the dropping of the arms embargo was a “step in the right direction”, though a spokesman for another grouping, the Syrian National Coalition, said the move might be “too little too late”.
Mr Ryabkov said Russia was disappointed by the decision. “This directly harms the prospects of convening an international conference,” he said.
More than 80,000 people have been killed and 1.5 million have fled Syria since the uprising against Mr Assad began in 2011, according to UN estimates.