US Defence Secretary Jim Mattis has formally returned church bells to the Philippines that were taken as war trophies over a century ago following gruesome clashes, seeking to close a contentious chapter in the two allies' shared history.

The decision to return the Bells of Balangiga to the Philippines ends a decades-long quest by Manila, including by President Rodrigo Duterte, and is expected to bolster US-Philippines' relations.

But it has upset some US veterans and Wyoming's delegation to the US Congress, which uniformly opposed returning bells that were a memorial to the 45 US soldiers who were killed during a surprise attack on September 28, 1901, in the central town of Balangiga.

Two of the three bells have been on display at FE Warren Air Force Base in Wyoming. The third bell is at a US Army museum in South Korea.

Mattis, speaking at a ceremony at the air force base attended by the Philippines ambassador to the US, said the Philippines has proven itself as a great US ally in conflicts over the century since that clash. He said the sacrifices of US forces would not be forgotten.

"To those who fear we lose something by returning these bells, please hear me when I say: Bells mark time, but courage is timeless," Mattis said. "It does not fade in history's dimly lit corridors."

In Manila, the Philippines' foreign affairs department cheered the move.

Wyoming's Congressional delegation, which did not attend the ceremony, issued a terse statement opposing oppose the efforts to move the bells.

All three bells will be restored and handed over to the Philippines as early as December.

The 1901 attack in Balangiga, on the Filipino island of Samar, was seen as perhaps the worst routing of US soldiers since the Battle of Little Bighorn in 1876, also known as Custer's Last Stand.

According to historians, one or more of the church bells were rung to signal the attack in Balangiga.

US forces took the bells after a brutal counterattack that killed anywhere from hundreds to thousands of people in the Philippines, historians say.

One US general was said to have directed his troops to "make the interior of Samar a howling wilderness."