Secretary of War Elihu Root responded to the charges of brutality: "The war in the Philippines has been conducted by the American army with scrupulous regard for the rules of civilized warfare… with self-restraint and with humanity never surpassed."

In Manila, a Marine named Littletown Waller, a major, was accused of shooting eleven defenseless Filipinos, without trial, on the island of Samar. Other marine officers described his testimony:

The major said that General Smith instructed him to kill and burn, and said that the more he killed and burned the better pleased he would be; that it was no time to take prisoners, and that he was to make Samar a howling wilderness. Major Waller asked General Smith to define the age limit for killing, and he replied "Everything over ten."

In the province of Batangas, the secretary of the province estimated that of the population of 300,000, one-third had been killed by combat, famine, or disease.

Mark Twain commented on the Philippine war:

We have pacified some thousands of the islanders and buried them; destroyed their fields; burned their villages, and turned their widows and orphans out-of-doors; furnished heartbreak by exile to some dozens of disagreeable patriots; subjugated the remaining ten millions by Benevolent Assimilation, which is the pious new name of the musket; we have acquired property in the three hundred concubines and other slaves of our business partner, the Sultan of Sulu, and hoisted our protecting flag over that swag.

And so, by these Providences of God — and the phrase is the government's, not mine — we are a World Power.

American firepower was overwhelmingly superior to anything the Filipino rebels could put together. In the very first battle, Admiral Dewey steamed up the Pasig River and fired 500-pound shells into the Filipino trenches. Dead Filipinos were piled so high that the Americans used their bodies for breastworks. A British witness said: "This is not war; it is simply massacre and murderous butchery." He was wrong; it was war.

For the rebels to hold out against such odds for years meant that they had the support of the population. General Arthur MacArthur, commander of the Filipino war, said: "… I believed that Aguinaldo's troops represented only a faction. I did not like to believe that the whole population of Luzon — the native population, that is — was opposed to us." But he said he was "reluctantly compelled" to believe this because the guerrilla tactics of the Filipino army "depended upon almost complete unity of action of the entire native population."

Despite the growing evidence of brutality and the work of the Anti-Imperialist League, some of the trade unions in the United States supported the action in the Philippines. The Typographical Union said it liked the idea of annexing more territory because English-language schools in those areas would help the printing trade. The publication of the glassmakers saw value in new territories that would buy glass. The railroad brotherhoods saw shipment of U.S. goods to the new territories meaning more work for railroad workers. Some unions repeated what big business was saying, that territorial expansion, by creating a market for surplus goods, would prevent another depression.

On the other hand, when the Leather Workers' Journal wrote that an increase in wages at home would solve the problem of surplus by creating more purchasing power inside the country, the Carpenters' Journal asked: "How much better off are the workingmen of England through all its colonial possessions?" The National Labor Tribune, publication of the Iron, Steel, and Tin Workers, agreed that the Philippines were rich with resources, but added:

The same can be said of this country, but if anybody were to ask you if you owned a coal mine, a sugar plantation, or railroad you would have to say no… all those things are in the hands of the trusts controlled by a few…

When the treaty for annexation of the Philippines was up for debate in Congress in early 1899, the Central Labor Unions of Boston and New York opposed it. There was a mass meeting in New York against annexation. The Anti-Imperialist League circulated more than a million pieces of literature against taking the Philippines. (Foner says that while the League was organized and dominated by intellectuals and business people, a large part of its half-million members were working-class people, including women and blacks.) Locals of the League held meetings all over the country. The campaign against the Treaty was a powerful one, and when the Senate did ratify it, it was by one vote.

The mixed reactions of labor to the war — lured by economic advantage, yet repelled by capitalist expansion and violence — ensured that labor could not unite either to stop the war or to conduct class war against the system at home. The reactions of black soldiers to the war were also mixed: there was the simple need to get ahead in a society where opportunities for success were denied the black man, and the military life gave such possibilities. There was race pride, the need to show that blacks were as courageous, as patriotic, as anyone else. And yet, there was with all this the consciousness of a brutal war, fought against colored people, a counterpart of the violence committed against black people in the United States.

Willard Gatewood, in his book Smoked Yankees and the Struggle for Empire, reproduces and analyzes 114 letters to Negro newspapers written by black soldiers in the period 1898–1902. The letters show all those conflicting emotions. Black soldiers encamped in Tampa, Florida, ran into bitter race hatred by white inhabitants there. And then, after they fought with distinction in Cuba, Negroes were not rewarded with officers' commissions; white officers commanded black regiments.

Negro soldiers in Lakeland, Florida, pistol-whipped a drugstore owner when he refused to serve one of them, and then, in a confrontation with a white crowd, killed a civilian. In Tampa, a race riot began when drunken white soldiers used a Negro child as a target to show their marksmanship; Negro soldiers retaliated, and then the streets "ran red with negro blood," according to press dispatches. Twenty-seven Negro soldiers and three whites were severely wounded. The chaplain of a black regiment in Tampa wrote to the Cleveland Gazette:

Is America any better than Spain? Has she not subjects in her very midst who are murdered daily without a trial of judge or jury? Has she not subjects in her own borders whose children are half-fed and half-clothed, because their father's skin is black… Yet the Negro is loyal to his country's flag.

The same chaplain, George Prioleau, talks of black veterans of the Cuban war "unkindly and sneeringly received" in Kansas City, Missouri. He says that "these black boys, heroes of our country, were not allowed to stand at the counters of restaurants and eat a sandwich and drink a cup of coffee, while the white soldiers were welcomed and invited to sit down at the tables and eat free of cost."

But it was the Filipino situation that aroused many blacks in the United States to militant opposition to the war. The senior bishop of the African Methodist Episcopal Church, Henry M. Turner, called the campaign in the Philippines "an unholy war of conquest" and referred to the Filipinos as "sable patriots."

There were four black regiments on duty in the Philippines. Many of the black soldiers established rapport with the brown-skinned natives on the islands, and were angered by the term «nigger» used by white troops to describe the Filipinos. An "unusually large number" of black troops deserted during the Philippines campaign, Gatewood says. The Filipino rebels often addressed themselves to "The Colored American Soldier" in posters, reminding them of lynchings back home, asking them not to serve the white imperialist against other colored people.