Although a quarter-century has passed since they were first displayed, the five murals Mark Rothko painted for Harvard remain a source of controversy and embarrassment at the university. Fingers have been pointed toward various factions in the Harvard administration and at the artist himself, but no matter where blame rests, the reasons for distress can clearly be seen: What Rothko donated to the university to cover the walls of a penthouse dining room intended for ceremonial functions has been irreparably damaged by overexposure to the sun. Lush crimson-toned paintings have faded to a variety of unrelated blue colors; they cannot be restored, The murals, which have also been ripped, spattered with food and marred by graffiti, were retired to storage nine years ago from the room in the Holyoke Center where they had been hung, their battered canvases a lingering humiliation to the university that had requested them. Plans to clean the panels and to install three of them in the school's Arthur M. Sackler Museum got far enough that the building's architect, James Stirling, included a niche for them in his plan.

But when doubts were raised by the Rothko Foundation and Rothko scholars about the intended placement of the murals in the museum and about the appropriateness of hanging only three of the five works that made up the ensemble, Harvard decided instead to stage at the Sackler a two-month exhibition of the complete cycle, arranged on the walls of one room to simulate the original configuration at the Holyoke Center. The show opened Aug. 6 and is to close Oct. 2, after which the painstakingly cleaned, restretched yet permanently discolored paintings will be returned to dark storage. Legacy of Skepticism

The exhibition - organized by Marjorie B. Cohn, the chief conservator at Harvard's Center for Conservation and Technical Studies -brings into sharp focus not only a legacy of skepticism toward modern art at this tradition-bound university but also a much broader issue concerning the fragility of 20th-century paintings and sculptures. Widespread experimentation with materials by many of this century's artists has produced physically unstable objects. Rothko's unwitting use of a fugitive pigment, Lithol Red, as the dominant color in his Harvard murals all but assured the fading that followed.

To underscore this point, and perhaps to deflect some blame from the university itself, the exhibition presents in test panels and in catalogue essays extensive evidence of the inevitable effects of both sunlight and the passage of time on the paints Rothko used, even under conditions less damaging to the murals than those at the brightly lighted Holyoke Center penthouse.