President William McKinley was furious about the press leak, fearing that it would damage negotiations with Spain.  He was also increasingly conscious that the War Department's administration of the conflict was a political liability in a congressional election year.  Criticism of Secretary of War Russell Alger surfaced as early as May and intensified as more horror stories about sanitary and health conditions appeared in the press.  Over the next several months, McKinley worked to deflect blame from the executive branch, while Alger firmly denied culpability.

The demobilization of Santiago was accomplished in just over three weeks in August, with soldiers sent to a makeshift camp near Montauk Point, Long Island.  The rapidity of the project meant the first troops to arrive received short rations, inadequate housing, and limited health care, all of which was reported in the press.  By the end of the month, the red tape had been cut and the problems at the camp largely resolved, but the images of suffering soldiers remained vivid to many Americans.  

There was also trouble at the volunteer camps in Georgia, Florida, and near Washington, D.C., where substandard conditions in poor locations led to disease, overcrowded hospitals, and low morale.  By mid-August, a typhoid epidemic was ravaging the camps.  The War Department expanded the medical facilities and moved troops to other camps.  The disease finally ran its course, but not before 2500 men died.

President McKinley visited the sick servicemen, refused public comment on his secretary of war, and appointed a presidential commission, headed by General Grenville Dodge, to investigate the War Department's conduct.  By appointing the commission, McKinley strategically placed himself on the side of justice, while distancing himself from the blame and eliminating the need for a congressional probe.  The Dodge Commission began its work in late September 1898, thereby minimizing political damage through the November elections.

The Dodge Commission's hearings did not reveal any problems that had not already been known.  In late December 1898, however, after tersely answering the commissioners' questions, General Nelson Miles gave a lengthy newspaper interview in which he charged that the canned beef provided to the servicemen had been doctored with chemicals, which caused the supply to spoil and make the troops who ate it ill.  

In January 1899, the Army's commissary general, Charles Eagan, irately responded, "I wish to force the lie back into his throat, covered with the contents of a camp latrine."  In February, a court martial convicted Eagan of insubordination for using hostile language against a superior, but McKinley reduced his sentence to suspension from duty and rank, but with full pay, for six years (preceding his retirement).  Although the "embalmed beef" scandal remains associated with the Spanish-American War even to the present, the Dodge Commission and a Senate investigation found the charges to be groundless.

The final report of the Dodge Commission criticized the War Department's overall lack of efficient administration and discipline during the war, but pointed to longstanding organizational problems in the U.S. military as the basic culprit.  Their findings helped secure passage of a military reform bill.  Secretary Alger and others were cleared of all corruption charges.  Nevertheless, McKinley had concluded the previous December that Alger was a political albatross who had to go.  Asking for the secretary's resignation, however, would imply the administration's guilt.  

In June 1899, Alger, who hoped to be elected to the U.S. Senate from Michigan, publicly voiced his support for the state's governor, who was a political enemy of the president.  An angry McKinley dispatched Vice President Garret Hobart to inform the secretary of war that it was time to leave office.  On July 19, Alger submitted his letter of resignation to the president, and Elihu Root, a lawyer from New York, replaced him.  Alger was not elected to the Senate in 1900, but was appointed to it in September 1902 upon the death of one of the Michigan senators.  He served until his own death in 1907.