"The work was finished a day ago," Shoigu said. He also added that it will take three months to train Syrian personnel to operate the system.
Earlier, it was reported that two Russian Air Force 124 Antonov military aircrafts landed in the Russian base near Latakia, transporting equipment and logistics, which had allegedly been loaded onto the planes along the way.
"We have not changed our strategic line on Iran," Education Minister Naftali Bennett said on Tuesday in response to the delivery of the system.
"We will not allow Iran to open up a third front against us. We will take actions as required," he told Israel Radio.
Russia announced last week that it would supply the anti-aircraft missiles after Syrian forces responding to an Israeli airstrike on September 17 mistakenly shot down a Russian military reconnaissance plane, killing all 15 people on board.
The friendly fire incident sparked regional tensions. Prime Minister Benjamin Netanyahu called Russian President Vladimir Putin to express sorrow at the loss of life and sent a high-level military delegation to Moscow.
Russian Foreign Minister Sergey Lavrov later was asked about the S-300s at a news conference and responded: "The deliveries started already."
He added that "the measures we will take will be devoted to ensure 100 percent safety and security of our men in Syria, and we will do this."
A spokesman for a Russian company producing electronic warfare systems says that their deployment to Syria will help protect the country's air defense assets and fend off enemy air raids.
Vladimir Mikheyev of Radioelectronics Technologies said Friday in remarks carried by the Interfax news agency that Krasukha and Zhitel electronic countermeasure units will place Syria's air defenses under an "electronic umbrella," making it hard to spot and attack them.
Moscow also said it will start using electronic countermeasures to jam any aircraft that would try to launch attacks off Syria's coast.
On Monday, Russian Defense Minister Sergei Shoigu said that the S-300 delivery and is intended to "calm down some hotheads" whose actions "pose a threat to our troops."
"In 2013, we agreed to stop the transfer of the system to Syria due to an Israeli request. However, through no fault of our own, the situation has changed," the defense minister stressed.
Later that day, Krelmin spokesman Dmitry Peskov told journalists on a conference call that the decision to supply the weapons was "not directed at any third country". "Russia needs to increase safety of its military and it should be clear for everyone," he said.