The Food and Drug Administration has reached a “critical point” in its struggle to oversee specialty pharmacies that have been associated with mounting illnesses and deaths, the head of the agency said Friday.

FDA Commissioner Margaret Hamburg’s comments came in response to a Washington Post investigation that found that shoddy practices and unsanitary conditions at three large-scale specialty pharmacies have been tied to deaths and illnesses over the past decade. Those safety lapses occurred long before national attention focused on New England Compounding Center (NECC), the Massachusetts company whose tainted steroid shots were at the center of last fall’s deadly meningitis outbreak.

Hamburg said the agency needs new, stronger and clearer legislation to oversee “firms engaged in large-scale distribution” of custom-mixed, or compounded, drugs, some of which were highlighted in the Post article. The current patchwork of federal and state laws is too weak to protect patients in all 50 states from high-risk compounding operations, she said in a statement.

“We’ve reached a critical point on this issue,” Hamburg said.

Rep. Edward J. Markey (D-Mass.), who released a report last fall showing uneven oversight by state authorities, said Friday that the FDA needs greater authority. He plans to reintroduce legislation that would allow the agency to regulate compounders that act more like drug manufacturers.

Here are basic steps a compounder could follow to make a drug.

“These compounding pharmacies have been operating under the radar for too long,” he said in a statement.

Pharmacies traditionally have mixed drugs to meet the specific needs of individual patients. But over the past two decades, compounding has become dominated by 15 companies that mass-produce medications and ship them to hospitals and clinics across state lines. The shipments are often based on anticipated needs, not on individual patient prescriptions.

Three of these large compounders, in addition to NECC, have experienced significant safety problems over the past decade that were tied to at least 39 illnesses, according to the Post’s analysis of hundreds of records and dozens of interviews. Two firms’ missteps were linked to at least six deaths. The problems included medications that were too potent or laced with bacteria.

The three companies are California-based Central Admixture Pharmacy Services, Illinois-based PharMEDium Services, and Texas-based ApotheCure. Officials of the companies have said that their firms produce safe, quality medications and adhere to the industry’s highest standards.