The F.D.A. said patients were not at risk, and that the treatment could still be sold.

But the news that a drugmaker had manipulated or mishandled data is an unsettling moment for the pharmaceutical industry. Many companies are racing to develop breakthrough gene therapy treatments for rare and intractable diseases.

And the F.D.A. has granted a record number of expedited approvals for novel drugs and treatments in recent years, and Zolgensma was among those given top priority.

Dr. Peter Marks, director of the F.D.A.’s Center for Biologics Evaluation and Research, said the drug’s approval probably would have been delayed had the agency known of the manipulated data. The public “expects us to have accurate data when we approve products,” he added.

Dr. Marks said the F.D.A. would continue to investigate and would determine whether Novartis should face civil or criminal penalties.

Shares of Novartis, a Swiss drugmaker that also makes the multiple sclerosis drug Gilenya, were down 2.77 percent, at $88.22 a share, on Tuesday.