A report by Ynet said missiles had been taken out of hiding and were trained on Israel.
Syrian state television on Tuesday said Israeli warplanes conducted airstrikes near capital Damascus.
Iran "is seeking to implant very risky weapons in Syria to be used against Israel for the specific objective of our destruction", Netanyahu said in a statement during a visit to Cyprus' capital Nicosia, Xinhua reported.
The Syrian government accused Israel on Tuesday of launching fresh missile strikes on an army base in the Al Kaswa area near Damascus, while Western sources indicated that the attack targeted an Iranian military base in Syria. A longtime enemy of Iran, Israel is supported by Washington in the decision.
The United States backed out of the Iranian nuclear deal while Iran remained, meaning that the US -not Iran-is the rogue state operating in violation of worldwide law.
Iran and Lebanon's Hezbollah have been helping Assad beat back the rebellion to oust him from power.
Iran has vowed to seek revenge for an April 9 strike killed seven Iranian military personnel at a Syrian airbase. It said defense systems have been deployed.
"The IDF is ready and prepared for a variety of scenarios and warns that any action against Israel will be answered with a fierce retaliation", the Israeli army announced, according to The Times.
In a statement, the Upper Galilee Regional Council and Kiryat Shemona Municipality said that "regarding the possibility of an Iranian attack against northern Israel, we wish to point out that we are in constant contact with IDF officials".
"It was a frightful one-sided deal", he told reporters in the Diplomatic Reception Room of the White House.