He claims the tainted cookies were made by another Da Vinci Charter Academy student two weeks ago and given to others.
The supposedly ash-laden sugar cookies were handed out to nine students, police said, but they were unsure of how many students were involved in distributing them.
Nobody has suffered any ill effects, and cremated human remains are not poisonous, although Davis Police lieutenant Paul Doroshov told The Sacramento Bee "there could be some emotional issues experienced".
"I hope this is just a huge misunderstanding", wrote one person on Twitter, while another said, "I don't think they broke any laws".
"And I was really, I was kind of horrified", he said.
He told the news organisation that the girl had previously offered to give him her grandfather's ashes if he changed seats with another student.
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The male student's mother, who requested the identities of her family members not be revealed, said she was extremely disappointed with the way the school handled the incident.
The Davis Joint Union School District later issued a statement, saying it couldn't comment on confidential student matters.
Police are looking into reports that two students had cooked up the morbid prank, but Lt Doroshov said he is not sure what charges, if any, the culprits would face.
Police are investigating, but have been unable to prove that human remains were baked into the cookies.
"They're juveniles and it's not a heinous or serious crime", he said.
The evidence so far comes from student testimony, authorities said.
He explained that whenever any wrongdoing occurs, the school applies disciplinary measures and restorative measures to restore any harm caused within the school community.
In a statement sent to parents, Principal Tyler Millsap said the school responded appropriately to what was a "particularly challenging" situation.