In a letter sent Monday to Air Force Secretary James Roche, the senators accused the academy's current leadership of not dealing with sexual abuse at the school.
"Despite warnings and clear indications that remedial action was needed, these officers failed to take effective action to correct these problems," Warner, R-VA, and Allard, R-CO, wrote in the letter.
The Air Force has two investigations underway into allegations that female cadets were reprimanded or ostracized for reporting sexual assaults. The Defense Department's inspector general plans to start its own investigation by the end of March.
The senators want the Air Force to consider assigning a female officer to one of the school's top posts - superintendent or commandant, according to Allard's spokesman Dick Wadhams.
Air Force Academy spokeswoman Pam Ancker said school officials would not comment until the Air Force released a report later this week on the abuse allegations.
The Air Force says there have been at least 56 reports of sexual assaults of female cadets over the last decade. Allard earlier rejected calls for replacing the commanders, saying it could be an excuse for resolving the real problems at the academy.
Lt. Gen. John Dallager has been academy superintendent since June 2000 and was scheduled to retire this summer, and Brig. Gen. Sylvanus Taco Gilbert has been commandant since 2001. The Air Force has said the two would not lose their jobs because the problems predate their leadership.
Dallager and Gilbert "have been energetic in helping the Air Force leadership address current problems," Roche and Air Force Chief of Staff Gen. John Jumper said in a recent statement.
Earlier this month, Roche said few, if any, female officers would be qualified to lead the academy, where about 15 percent of the cadets are women.
Superintendents usually are three-star generals and commandants have typically been one-star generals or colonels who get their first star while at the academy. Currently, the Air Force only has one female three-star general, Lt. Gen. Leslie Kenne, at headquarters in Washington, D.C.
Warner and Allard wrote their letter on behalf of the Senate Armed Services Committee. The House Armed Services Committee was also planning to look into the allegations. U.S. Rep. Tom Tancredo R-CO, has already called for the dismissal of top academy commanders.
A civilian investigation is also underway by the El Paso County District Attorney's office at the request of an alleged victim.
By Colleen Long