Suspect One Goh became upset because officials would not fully refund his tuition for the nursing program, Jaehoon Moon, chief operating officer of Oikos University, told KGO-TV.
The amount in dispute was $4,000 to $6,000, according to Moon, who said officials had offered partial reimbursement.
The disclosure came as police said they had located a .45-caliber semiautomatic handgun they believe was used in the attack on Monday.
The weapon was found in the shallow waters of a tributary of San Leandro Bay, about a half-mile from the school. Its serial numbers match a gun purchased by Goh, city spokeswoman Cynthia Perkins said.
During the meetings with school administrators, the 43-year-old Goh also complained that he didn't get along with his classmates, so officials offered to transfer him to another classroom, Moon said.
They believed the issue was resolved and Goh would restart classes. However, police said Goh returned to the school on Monday, killing six students and a school secretary while wounding three others.
Nursing program director Ellen Cervellon previously said she met several times with Goh over the tuition issue and that he said students had been picking on him.
Police have said Goh was targeting a female administrator when he went to his former school, and opened fire when he learned she wasn't there.
Police are investigating whether Goh was seeking multiple targets. Cervellon told The Associated Press that she believed she was the intended target.
However, Police Chief Howard Jordan later said the main target was a woman who no longer works at Oikos.
Goh is charged with seven counts of murder and three counts of attempted murder with a special circumstance allegation that could make him eligible for the death penalty. He has not entered a plea.
At the Oikos campus, workers cleaned the building behind police tape. A banner draped at the school's front entrance read, "In Memoriam, Forever United In Life, April 2, 2012." It listed the names of the victims, followed by the words: "We Will Remember. We Will Prevail."
Students were being allowed back on campus, but classes won't resume for several weeks, Acting Vice President Nam Soo Woo said.
Several students were escorted by police into the school on Thursday to retrieve belongings. It was their first time in the school since Monday.
As he waited his turn, Tenzin Topchen, 26, tried to calm his lingering fears.
"I'm nervous, very nervous," Topchen said before quickly gathering his items and driving off in his car, which had been parked behind the school for three days.
Dechen Yangdon, 27, also waited nervously before two investigators took her inside. She is being hailed as a hero for intuitively locking a classroom door and turning off the lights after hearing gunshots. The shooter tried kicking in the door then fired at it. No students were injured.
Investigators who walked Yangdon inside the school shook her hand and praised her.
Asked what it was like being back inside the school, Yangdon gave a blank stare, bowed her head, grabbed her husband's hand and quickly walked away.
