TOKYO — The top U.S. military official in Japan said today that the alleged slaying of a Japanese woman by a Navy sailor was "horrific" and has challenged the two countries' military alliance.

Earlier in the day, however, the two nations said Tokyo would spend $1.2 billion in 2006 and 2007 to help cover the costs of keeping tens of thousands of U.S. troops in this country, and stressed that despite concerns over the slaying their bilateral ties are strong.

Japanese authorities say William Oliver Reese, 21, fatally beat and robbed a Japanese woman of about $130 near a U.S. Navy base southwest of Tokyo on Jan. 3. He has been turned over to Japanese custody.

"The alliance is a partnership," Lt. Gen. Bruce Wright told a news conference. "This alliance has just been significantly challenged. It's horrific. It's horrible."

Wright, head of the U.S. Forces in Japan, said he would instruct commanders to work harder toward a goal of "zero criminal incidents" involving American service personnel in Japan.

The murder has rekindled lingering concerns over crime related to the roughly 50,000 U.S troops stationed here under a mutual security pact. Such concerns boiled over into huge protests after the rape of a schoolgirl on the island of Okinawa in 1995.

Learning from experience, U.S. officials have been quick to express their regrets. Wright even attended the wake for the slain woman.

The killing comes at a crucial time for the alliance.

Tokyo and Washington recently agreed on a sweeping realignment of the U.S. troops here, including the movement of 7,000 Marines off the southern island of Okinawa. The plan would also station a U.S. nuclear-powered aircraft carrier in Japan for the first time.

Officials say the changes will streamline and strengthen the alliance, but talks continue over many of the details. In particular, the possibility of shutting down a Marine air station and building a new airstrip elsewhere within Okinawa has provoked strong local opposition.

Still, Japan's official support for the U.S. troops here remains strong.

The $1.2 billion in annual support announced today will be used to pay the 23,000 local employees on U.S. military bases in Japan, along with 85 percent of the utility costs on the facilities. It was roughly equal to what Japan paid in 2004.

The agreement was signed today by Japanese Foreign Minister Taro Aso and visiting Deputy Secretary of State Robert Zoellick, according to a statement released by the U.S. Embassy.