Military police are investigating claims that two officer cadets "waterboarded" a fellow recruit at Sandhurst Academy.
Brigadier Bill Wright, commander of the Berkshire military college, ordered the probe into the alleged incident on August 7.
A cadet was allegedly pinned down before water was poured over a cloth covering his face, according to The Sun.
Both Prince William and Prince Harry attended Sandhurst, where all officers in the British Army are trained.
Brig Wright said: "I am aware of allegations about an incident at the Royal Military Academy Sandhurst on August 7 involving some of our officer cadets.
"I have ordered an investigation by the Royal Military Police.
"The Army and I expect the highest standards of behaviour at Sandhurst; anyone found to have fallen short is dealt with robustly, including dismissal, if appropriate."