The effort to hide its capability complicated the West's military and geopolitical calculus and helped shield Tehran from attack, US reports said.
The Obama administration is pressing for strong and immediate new sanctions against Tehran over its nuclear program. Analysts told The New York Times that Iran's tunnelling - which Tehran calls a strategy of "passive defence" - was a crucial factor behind the push for non-military solutions to the issue.
The report said US Secretary of Defence Robert Gates had discounted the possibility of a military strike against Iran, in the belief it would only slow Tehran's nuclear program by one to three years while driving the project further underground.
"It complicates your targeting," Richard L. Russell, a former CIA analyst now at the National Defence University, told the paper yesterday. "We're used to facilities being above ground. Underground, it becomes literally a black hole. You can't be sure what's taking place."
US government and private experts told the paper there were hundreds, perhaps thousands, of tunnels in Iran, and that the lines separating their use could be fuzzy. Companies owned by the Islamic Revolutionary Guards Corps of Iran, for example, built civilian as well as military tunnels.
No one in the West knows how much, or exactly what part of Iran's nuclear program lies hidden in the tunnels.
The report said the original hub of the nuclear complex at Isfahan consisted of scores of buildings that were easily observed and easy to attack, but US government analysts said that in recent years Iran had honeycombed the nearby mountains with tunnels. Satellite photos showed six entrances.
But the Obama administration has been careful to leave the military option on the table against Iran, and the Pentagon is racing to develop a deadly tunnel weapon. The report said the device - seven metres long and called the Massive Ordnance Penetrator - began as a 2004 recommendation from the US Defence Science Board, a high-level advisory group to the Pentagon.
It underwent preliminary testing in 2007, and its first deployment is expected in the northern summer. It will be carried by the B-2 stealth bomber.
The report yesterday came as a Pentagon-sponsored study by the Rand Corporation said the Revolutionary Guards had "gained primacy" in Iran since the 2009 presidential election.