Iran has the largest ballistic missile force in the world, often said to be a key component of its military deterrent, and also fields large numbers of low-flying cruise missiles, which it is constantly upgrading.
"The intelligence unit of the Defence Ministry thwarted one of the largest sabotage plots targeting Iran's missile, aviation and airspace military industry," Iranian state TV said. "This sabotage was carried out under the guidance of the Zionist intelligence services and their agents."
Citing an unnamed source, state media said a network of Israeli spies had aimed to introduce defective parts into the production of advanced missiles.
There was no immediate response from Israel.
Hossein Amirabdollahian was speaking during a visit to the Syrian capital.
His warning came two days after air strikes blamed on Israel hit the international airport in Aleppo.
Mr Amirabdollahian, who held meetings with Prime Minister Hussein Arnous and Foreign Minister Faisal Mekdad, described Syria as “an ally of Iran” and Iran as “a friend of Syria during the Arab country’s difficult times”.
The air strikes damaged the runway at Aleppo's airport, putting it out of service. The airport has been targeted several times this year, including two attacks in March that put it out of service.
“The criminal practices by the Zionist entity in the region will not remain without retaliation,” Mr Amirabdollahian said at a press conference with Mr Mekdad in Damascus.
Israel has carried out hundreds of strikes on targets in government-controlled parts of Syria in recent years, but it rarely acknowledges or discusses the operations.
The strikes often aim at Syrian military forces or Iran-backed groups.
Tehran has been a main backer of the Syrian government since a 2011 uprising turned into a civil war.
It has sent thousands of fighters to Syria, helping to tip the balance of power in the favour of President Bashar Al Assad.
Israel has damaged air and seaports in the government-held parts of Syria in an apparent attempt to prevent arms shipments from Iran to militant groups backed by Tehran, including Hezbollah in Lebanon.
Mr Amirabdollahian also called for the withdrawal of US forces from Syria, describing their presence in the country as illegal. Hundreds of American troops are posted in north-east Syria to support anti-ISIS operations by allied Syrian forces.
“We advise US forces to return home, and we also advise American authorities to leave the region to the people of the region,” the Iranian minister said.
Mr Amirabdollahian also spoke about the recent string of public desecrations of the Quran by a handful of anti-Islam activists in Denmark.
He said Denmark's Foreign Minister told him that the government planned to make it illegal to desecrate any holy book.
“We welcome this move and we advise Sweden and other European countries to respect religions and holy books,” Mr Amirabdollahian said.
The desecrations of Islam's holy text sparked protests across the Muslim world, some of them violent.