The report sent to the university Friday accuses Sampson of five major violations, including the allegation of providing "false or misleading information" to university officials and NCAA enforcement staff. The school contended in its initial report that all violations were secondary infractions.
But the NCAA accused Sampson of failing "to deport himself ... with the generally recognized high standard of honesty" and failing to promote an atmosphere of compliance within the men's basketball program, categorized as major infractions.
Athletic director Rick Greenspan promised the university would cooperate with NCAA requests.
"We are extremely disappointed in these new allegations regarding coach Sampson," Greenspan said in a statement. "To say the least, we view these allegations with grave concern."
Attempts to reach Sampson's attorney, Matt Kramer, were unsuccessful. The NCAA declined comment.
Indiana has until May 8 to provide a written response to the report. The report says that Indiana officials will be required to appear June 14 in Seattle at a hearing before the Division I infractions committee.
Indiana has not had a major NCAA violation in any sport since 1960.
The report comes more than three months after the university announced an internal investigation found Sampson made more than 100 impermissible phone calls while still on NCAA probation for similar infractions at Oklahoma.
Sampson first got in trouble with the NCAA for making 577 impermissible calls from 2000 to 2004 and was sanctioned by the NCAA in May 2006, less than two months after taking the Indiana job. He was banned from calling recruits and making off-campus visits for a year.