Its ambassador to the UN said findings indicated Israel “was responsible for this attempted act of aggression”.
Iran, he said, reserves the right “to respond resolutely to any threats or wrongful actions” by Israel.
Israel has neither confirmed nor denied it was behind the attack, which Iran said caused minor damage, though this has not been independently verified.
The two countries are arch-foes and in recent years have been engaged in what has been described as a “shadow war” of unclaimed attacks on each other’s assets, infrastructure and nationals.
Israel is mostly known to have carried out strikes on what it says are Iranian weapons transfers to militants in Lebanon and is also believed to have sabotaged Iran’s nuclear sites and killed Iranian nuclear scientists. Iran, which rejects Israel’s right to exist, has been accused by Israel of attacking and planning to attack Israeli and Jewish targets and people. Each side is also believed to have attacked the other’s shipping.
In a letter to the UN secretary general, Iranian ambassador Amir Saeid Iravani accused Israel of “an attempt… to launch a terrorist attack against a workshop complex” belonging to Iran’s defence ministry. He did not specify what evidence Iran had for this.
Mr Iravani said Iran reserved the right to respond “wherever and whenever deemed necessary”.
The purpose of the attacked site is unclear, though reports suggest it could be connected to missile production.
US media have quoted unnamed US officials as saying Israel carried out the attack, which Iran said involved three drones, on Saturday night at about 23:30 (20:00 GMT). Iran said one was destroyed by air defence systems and two were caught by “defence traps”, causing minor damage to a building and no casualties.
If confirmed it would mark the first such known attack on a facility in Iran under the current Israeli government which came to power under Benjamin Netanyahu at the end of December.
In an interview with CNN on Tuesday, Mr Netanyahu said Israel had been “taking action against certain weapons development” in Iran, but neither confirmed nor denied it had attacked the site in Isfahan.
“I never talk about specific operations… and every time some explosion takes place in the Middle East, Israel is blamed or given responsibility – sometimes we are sometimes we’re not,” he said.