MANILA — Three church bells taken from the central Philippines as war booty by American troops more than a century ago were flown to their original home Tuesday, ending a contentious flash point in relations between the two longtime military allies.

The bells were turned over by Sung Kim, the American ambassador, to the Philippine government, which had stepped up its efforts to recover the war artifacts since President Rodrigo Duterte took office two years ago.

American troops seized the bells in 1901 from the town of Balangiga on Samar Island, where they went to avenge the death of 48 fellow soldiers killed in an attack by Filipino guerrillas on an American garrison. The American troops were under orders to turn the area into a “howling wilderness” by killing every male citizen age 10 or older and capable of bearing arms.

The massacre was the deadliest of American troops since Col. George Armstrong Custer and his troops were slaughtered at the Battle of Little Bighorn 25 years earlier.