Theranos is now under review by two federal regulators. In addition to the Centers for Medicare and Medicaid Services inspection, the Food and Drug Administration has curtailed its blood tests and analyses for all but one test, for herpes.

While Ms. Holmes has been insistent that the company will eventually win the necessary regulatory approvals, the letter from C.M.S. fosters continued skepticism over Theranos’s ability to perform these novel tests with a few drops of blood.

In its letter, dated Jan. 25, C.M.S., which is the regulator responsible for overseeing clinical laboratories, detailed five conditions that it said the Newark lab failed to meet. The deficiencies involve oversight and personnel at the lab and the systems used to analyze the tests, the agency said. It declined to comment further.

Much of the agency’s concern surrounded the oversight at the lab. Theranos said the company had made “policy and personnel changes” at the facility, including a new lab director, Dr. Kingshuk Das, a board-certified pathologist.

Theranos had been criticized by outside investors and industry experts for a lack of laboratory-trained executives both on its board and in its management of the company.

While the company must scramble to satisfy C.M.S., it has yet to demonstrate outside confidence in its testing. Walgreens, the drugstore chain that has a pilot program with Theranos in some clinics in Arizona, has not decided whether it will continue the program or commit to expanding the use of Theranos testing outside of Arizona.

For its part, Theranos has said that those discussions were still underway.

Even more important, however, the company has held out the promise of approval by the F.D.A. for myriad other tests besides the one for herpes that was approved last year.

The F.D.A. is also reviewing the company’s analysis machines and processes, and the agency’s approval is required for additional tests. While Theranos is able to use conventional methods to continue its testing, it remains unclear how much of its own technology the company is able to use while awaiting regulatory approval.