"I think it's an excuse. I hate to say that, but, you know, why would you choose two black girls?" Muhammad said Wednesday.
Alameda County District Attorney Nancy O'Malley said outside court that prosecutors are still investigating if Cowell was motivated by hate.
“It’s a very, very troubling case,” she said. “It’s a brutal, horrific murder and attempted murder, and for our whole community it’s an awful situation. And that’s why were treating it with the seriousness that we have.”
Cowell did not enter a plea and his arraignment on murder and attempted murder charges was set over to a future date.
Muhammad said his daughter was going to graduate "with very high honors" from Dewey Academy in December and planned to join the military.
"I should be planning her graduation, not her funeral," he said.
The San Francisco Chronicle on Tuesday detailed Cowell's violent past, a history that includes repeated episodes of violence and convictions for robbery, battery, assault with a deadly weapons and being under the influence of a controlled substance.
Cowell's family said in their statement he had been diagnosed with bipolar disorder and schizophrenia.
He was released from the Atascadero state mental hospital in May, but "there was not a place for him to go with most of the mental institutions being shut down," the family said. They added that "the system has failed in this instance."
"We had to get a restraining order at one time as well for our own protection. He was living on the streets without the proper treatment," the family said. "This is in no way an excuse for this senseless and vicious attack."
Cowell's mother, Anne Cowell, is serving a three-year sentence for setting fire to a transitional housing shelter in Santa Rosa, the Sonoma County Sheriff's Office said.
California Department of Corrections and Rehabilitation spokeswoman Vicky Waters said John Cowell had been under "active parole supervision and had no arrest warrants."
She said the agency is conducting a review and also cooperating with BART and local law enforcement in their investigation.
Cowell's family said it was "heartbroken" and mourning for the victims' family.
"This horrific tragedy never should have happened," the statement said.
