University officials said they would abide by the California Department of Public Health's finding that the voluntary gene scans must be treated as medical diagnostic tests if students are given access to their individual results.
In response, university officials said they would only report the combined test results of all students.
The university said it had sent test kits to more than 5,000 incoming freshmen and transfer students as part of its "Bring Your Genes to Cal" program.
New students typically are asked to read a book that can serve as a common point of discussion. The university this year decided to use the gene tests to spur conversation about genetics and personalized medicine.
The scans will analyze genes that help control the body's responses to alcohol, dairy products and folic acid. Organizers of the program said they specifically chose genes that were not connected to serious health issues.
But the health department said giving students access to their individual results still meant the labs performing the analyses must meet certain state and federal standards for medical testing.
The university planned to analyze the samples in a campus research lab.Mark Schlissel, dean of biological sciences at UC Berkeley, spearheaded the program. He said the school would follow the health department's interpretation of the law despite disagreeing with its findings.
"We believe this is a flawed reading of the statute that raises questions about who has control over teaching at the university, and in the broader sense, who has control over information about our own genes," Schlissel said.
The gene-scanning program immediately came under fire from biotechnology watchdogs and privacy advocates after it was announced in May. Critics said the program was pushing an unproven technology on impressionable students who could misinterpret the significance of their test results.
"This program was misconceived and hastily constructed from the beginning," said Jesse Reynolds, a policy analyst at the Center for Genetics and Society in Oakland.
The university's decision comes after state lawmakers held a hearing Tuesday to express concerns about the gene tests. Assemblyman Marty Block, who headed up the hearing as chair of the Higher Education Committee, said he welcomed the university's revised plan.