Brig. Gen. Johnny Weida, the commandant in charge of cadets, declined to name the cadet or detail possible charges.
"I am confident in our team," Weida said at a hastily called news conference a few hours before a speech by the chairman of the Joint Chiefs of Staff. "We will deal with that one cadet or maybe two and get it over with."
The senior cadet is accused of organizing a Web site that promoted group sex, sending e-mails to hundreds of people, and organizing and participating in sex sessions involving as many as two dozen men and one woman in nearby Colorado Springs and Denver, Weida said.
The investigation was first reported by a Denver television station.
Academy police seized the cadet's computer on Wednesday. Officials would not say whether the e-mails were sent from the academy, insisting their Internet system blocks pornography and gambling.
Weida said the Web site had been taken down, but would not comment on the length of time it had been in operation.
Weida said he expects the investigation to be completed before May 28, when the cadet is scheduled to graduate.
The school near Colorado Springs has been under scrutiny since dozens of female cadets said they were reprimanded or ostracized when they reported being raped. Weida took over three weeks ago after the academy's top officers were reassigned.
Three military investigations are under way and a civilian panel ordered by Congress will begin meeting later this month.
Word of the Internet investigation surfaced on the same day the chairman of the Joint Chiefs of Staff, Gen. Richard B. Myers, was visiting for a speech on the "The New American Way of War."
Myers did not refer specifically to the investigations in his address to about 2,000 cadets, saying he knew they had been through a lot lately, but have a lot to be proud of.
Lt. Col. Perry Nouis, an academy spokesman, said the latest development indicates there might still be problems to resolve. "We have to remember this is one cadet out of thousands, but everything can't change overnight," he said.
Sen. Wayne Allard, a Colorado Republican who heard from dozens of female cadets, said he believed the new academy leaders were taking this report seriously.
Kate Summers, a spokeswoman for the nonprofit Miles Foundation, which helps victims of violence in the military, said she would be disappointed if the allegations proved true.
"This is not behavior that would speak well to someone coming into command in the U.S. armed forces," she said.
By Colleen Long
By Colleen Long