The US Food and Drug Administration, responding to growing concerns that a host of tests for illnesses from cancer to Lyme disease may be inaccurately diagnosing patients, announced Thursday that it intends to regulate many of the tests. Thousands of tests on the market -- including some created in Cambridge and Greater Boston’s thriving biotech industry -- take advantage of a legal loophole that exempts their makers from FDA oversight and having to prove the tests do what they claim to.

In many cases, doctors and patients are left to decide which tests are legitimate. FDA commissioner Margaret Hamburg said during a news conference that while a new era of genetic tests offers great hope for patients, her agency was also aware of faulty tests, such as ones that have led cancer patients to receive inappropriate treatment and that purport to help diagnose autism. “These tests need to be safe and reliable,’’ said Hamburg.

The long-expected oversight will be phased in over nine years, with the first batch of highest-risk tests subject to FDA review a year after the proposed rules are finalized. At issue is what’s known as laboratory developed tests, or LDTs, which include many of the genetic tests developed since the human genome was first sequenced a decade ago. As long as these tests are designed, manufactured, and used in a single lab and not marketed directly to consumers they can be sold without FDA approval.

There have been several high-profile cases of problematic LDTs, including one for ovarian cancer that was pulled from the market. Earlier this year, the U.S. Centers for Disease Control and Prevention issued a warning to doctors not to use Lyme disease diagnostic tests unless they had been approved by the FDA, saying their accuracy had not been established. Lyme disease is a growing threat across the Northeast and an increasing number of labs offer LDT tests that critics say prompt some patients to take antibiotics unnecessarily, sometimes for years.

Members of the Massachusetts biotech industry reacted cautiously to the FDA proposal. “Our hope is ... the final product will reflect the need to provide high quality test results to patients and their families while still allowing innovative new tests be developed for clinical use in a timely fashion,’’ said Mary Ellen Cortizas, chief operating officer of Cambridge-based Claritas Genomics. The genetic-testing laboratory offers over 90 of these LDTs for childhood illnesses, including for muscular dystrophy and autism.

Lab developed tests were originally exempted from FDA oversight in the 1970s because most were low-risk variations on common tests or for rare diseases and offered in a hospital lab overseen by experts. In the last decade, however, an increasing number of for-profit companies are using the exemption to market ever-more-complex tests, such as to detect patients’ risk for breast cancer or Alzheimer’s disease, and prenatal screening tests that predict the likelihood a child will be born with Down Syndrome or other genetic conditions.

The FDA estimates there are about 2,000 labs offering more than 10,000 such tests in the United States today. The FDA said it intends to require makers of all laboratory developed tests to notify the FDA of their products and alert the agency of any problems with the tests. Tests that are considered the highest risk include some for conditions where an FDA-approved test already exists. Those will have to undergo a review to ensure they work.

Laboratory developed tests exempted from the review will include those to detect rare diseases and, in certain circumstances, ones for which there is no FDA-approved or cleared test. Alan Mertz, president of the American Clinical Laboratory Association, an industry group, said in statement that the tests are already overseen by other regulatory agencies and FDA oversight would result in patient harm.

These tests, he said, have “allowed labs to diagnose and measure disease with an accuracy and precision never before possible.’’ Some makers of the tests, however, welcomed the oversight. Cambridge-based Foundation Medicine Inc., which provides genetic profiles of tumors to help oncologists chose the best treatment for patients, said regulation was needed for high-risk tests. “(Foundation Medicine) welcomes the adoption of rigorous standards for LDTs where life-altering treatment decisions can be made based on the results of these tests,’’ the company said in a statement.

Senator Edward Markey, a Massachusetts Democrat, applauded the FDA for releasing the “long-overdue” proposed guidance. He, along with a group of other senators, recently sent the FDA a letter urging it to oversee the tests.