WASHINGTON — The U.S. military's shipment to Taiwan was supposed to be helicopter batteries.

But when the boxes arrived in fall 2006, they contained electrical fuses used in missile warheads, and it took the Pentagon nearly two years to figure out the mix-up. The shipment did not contain nuclear materials.

On Tuesday, the shipment to Taiwan of four of the classified fuses for an intercontinental ballistic missile set off a broad investigation into the security of Pentagon weapons and raised concerns over U.S. relations with China, which vehemently opposes U.S. arms sales to Taiwan.

Despite quarterly checks of the inventory, defense officials said they never knew the fuses were gone. Only after months of discussions with Taiwan over the missing batteries did the Pentagon finally realize — late last week — the gravity of what had happened.

Once the error was discovered, the military quickly recovered the four fuses. How it happened, and whether the incident constitutes a violation of any treaty or agreement governing international sales of missile technology, were lingering questions.

At a hastily called news conference Tuesday, Ryan Henry, the No. 2 policy official in Defense Secretary Robert Gates' office, said President Bush as well as Chinese leaders were informed of the mistake — an error Henry called intolerable.

"I cannot emphasize forcefully enough how strong the secretary feels about this matter and how disconcerting it is to him," Henry told reporters. He added that in an organization the size of the Defense Department, there will be mistakes, but that "they cannot be tolerated in the arena in strategic systems, whether they are nuclear or only associated equipment, as was in this case."

In a comment directed at the Chinese concerns, Henry said the error does not suggest that U.S. policies on arms sales to Taiwan have changed.

Taiwan, which split from China amid civil war in 1949, is the most sensitive issue in U.S.-China relations. Chinese officials repeatedly complained about U.S. arms sales to Taiwan during meetings with Gates in Beijing last fall. The U.S. insists it only provides weapons that would allow Taiwan to defend itself.

Beijing claims Taiwan as its own and has threatened to attack should the self-governing island make its de facto independence formal. Washington has hinted that it would go to war to protect Taiwan.

The nearly two-year saga of the fuse shipment began in August 2006.

According to Air Force Secretary Michael Wynne, the fuses, contained in four large shipping containers, had been sent from F.E. Warren Air Force Base in Wyoming to a Defense Logistics Agency warehouse at Hill Air Force Base in Ogden.