Defense analysts believe Israel has been targeting the Islamic Republic's computer networks, to gather intelligence on the nuclear program and also to launch cyber attacks against it.
"This has become a very important area in Israeli strategy, and it has to be taken into account," said Alon Ben David, an Israeli defense specialist. "It has become a more and more important element both for intelligence gathering but also for aggressive operations."
Experts believe Israeli intelligence agencies have been hacking into Iranian computer systems in an effort to disrupt or contaminate networks with viruses and malicious software.
"We came to the conclusion, for our purposes, a key Iranian vulnerability is in its online vulnerability," an unnamed recently retired member of Israel's security cabinet told the Reuters news agency. "We have acted accordingly."
The potential for hacking into foreign networks came to light over 10 years ago in Israel during a routine defense exercise. Israeli hackers managed to break into an Israeli oil and gas storage facility and officials were shocked to discover how vulnerable their computer systems had become.
Since then Israel has been upgrading defensive mechanisms against cyber attack but also developing offensive capabilities, and defense analysts believe Israel's thriving hi-tech commercial sector provides plenty of home-grown expertise.
One advantage of this secret war is that the attacker is difficult to identify, making retaliation much more difficult.
"You don't see fire and smoke," Israeli weapons expert Yiftar Shapir from the Israeli Institute for Security Studies said in an interview with ABC News. "Only when your computer stops working do you realize you are under attack. You can easily conceal your attack from the target and it's very difficult to trace."
Systems can be interfered with online or in the supply chain, since so much of the equipment and know how for the Iranian nuclear effort comes from outside sources. International defense experts believe both Israel and the United States have been trying to sabotage equipment before it gets delivered to the Iranians.
There have been several successes, according to Ben David. "The Iranians have experienced a number of malfunctions and unexplained breakdowns, all of which point to foreign interference in the supply chain for the program."
In a far more conventional military attack in September 2007 unidentified aircraft destroyed a suspected nuclear reactor in the Syrian desert. Israel has never publicly admitted it carried out the raid.
Ben David told ABC News there was also a critical cyber warfare element in ensuring the success of the mission. He declined to talk about who had carried it out.
"Syria has one of the region's densest and best-armed air defense systems, and yet not one attacking plane was detected and not one defensive missile was ever fired," he said.
Whatever success Israel's cyber war against Iran has achieved, most experts admit that at best it will only damage and delay Iran's progress towards nuclear capability. To destroy the program completely will require far more traditional weapons of war and attacks that will be far easier to trace.