Ray Bowen, the school's president, questioned the newspaper's motives for its public apology and the ensuing donation Monday.
"Texas A&M university will not allow itself to become an agent for The Arizona Republic as it tries to manage the public criticism it is receiving," Bowen wrote to the newspaper's editorial page editor. "For this reason, and out of respect for the victims of the bonfire tragedy, Texas A&M University will not accept money from The Arizona Republic."
Twelve students were killed Nov. 18 while building the bonfire pile, which traditionally is lighted the night before the annual University of Texas football game. The next day, the newspaper ran an editorial cartoon comparing the accident to the 1993 Branch Davidian siege near Waco and the 1998 dragging death of a black Jasper man.
In a letter accompanying the checks, Republic editorial page editor Keven Ann Willey acknowledged Steve Benson's cartoon "inappropriately linked the tragedy of deaths at Waco and Jasper" with the bonfire.
"Please accept the enclosed checks as tokens of the sincerity of our regret at having needlessly added to your community's pain and suffering," Willey said in the Dec. 1 letter.
The cartoon was retracted and pulled from the Republic's Web site. Willey wouldn't comment Tuesday.
Earlier Tuesday, campus flags were lowered to half-staff and a notice went up listing the names of the collapse victims, who were to be honored with a hallowed century-old campus tradition - Silver Taps.
Meanwhile, more than 1,000 people gathered Tuesday night in a solemn ceremony to remember the students who died.
Many stood for an hour or longer in the brisk night air, hands shoved deep into coat pockets or clasping the hands of loved ones.
Hymns pealed from a nearby tower, signaling the start of Silver Taps,a special arrangement of the military funeral song that follows a 21-gun salute fired by an honor guard.
As the echoes of the shots died away, buglers began to play Silver Taps.
©1999 The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed