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.

At some point in 2007 — exactly when is not clear — Wynne said that Taiwanese authorities notified U.S. officials that they did not get the batteries they had ordered. Discussions ensued for months, during which, "we, on our side, thought we were talking about different sorts of batteries. There was an effort to resolve and to reimburse them," said Henry.

Finally, late last week, U.S. military officials realized what had been shipped to Taiwan and worked immediately to get the fuses back. They have now been recovered.

White House press secretary Dana Perino said Bush "appreciates that they are taking action, and that there is a full investigation under way."

Asked whether Bush still has confidence in Air Force leadership, Perino said: "Yes, yes he does."

F.E. Warren spokesman Sgt. Kurt Arkenberg said it appeared that no one at the Cheyenne, Wyo., base was responsible for the mix-up.

Arkenberg said Hill is a repository for new and used aircraft and missile components, and parts are routinely shipped between there and F.E. Warren.

Col. Mike Morgan, commander of the 90th Space Wing at F.E. Warren, said in a statement that the Wyoming base has "stringent accountability procedures in place" for shipments to the Utah base.

Henry said that if the incident is a violation of any treaty or agreement, it was unintentional.

"We are being totally transparent. We have corrected the situation," he said. "The United States stands up to its treaty obligations and we're dealing with this in the most straightforward manner we can."

Christopher Hill, U.S. assistant secretary of state for East Asia, said the Chinese have been briefed by U.S. officials in Washington and Beijing.

"We told them what happened, because this was obviously an accident," Hill said after a speech in Washington. "We've been very transparent with them about what happened."

Gates has ordered a full investigation, and in a memo Tuesday he put Navy Adm. Kirkland H. Donald in charge and asked that Donald report back with an initial assessment by April 15.

Henry said an examination of the site in Taiwan where the components had been stored after delivery indicated that they had not been tampered with. He said the components were "quite dated," as part of a system designed in the 1960s.

The Chinese Embassy did not immediately respond to a request for comment. A Taiwan official said Tuesday that the island's diplomats in Washington typically do not comment on Defense Department matters.

The fuses were manufactured for use on a Minuteman strategic nuclear missile and are linked to the triggering mechanism in the nose cone, but they contain no nuclear materials.

This is the second nuclear-related mistake involving the military in recent months. Last August, an Air Force B-52 bomber was mistakenly armed with six nuclear-tipped cruise missiles and flown from Minot Air Force Base, N.D., to Barksdale Air Force Base, La. At the time, the pilot and crew were unaware they had nuclear arms aboard.