The Massachusetts specialty pharmacy linked to the deadly fungal meningitis outbreak knew it had extensive contamination by mold and bacteria throughout its operations for making sterile drugs but failed to take corrective action, federal health officials said Friday.

In the first nine months of the year, New England Compounding Center’s internal monitoring program showed mold or bacterial contamination at more than 80 locations, including numerous places in its “clean rooms” where sterile drugs are made. In more than half the cases, the company’s own testing showed bacteria and mold above its “action” limits, but there is no evidence that it took action, according to a report issued by the Food and Drug Administration.

The report is based on FDA inspections at the Framingham company after the recall of tainted steroid shots implicated in the outbreak.

The U.S. Centers for Disease Control and Prevention said Friday there were 338 cases, including 25 deaths, in 18 states.

The FDA report, known as a Form 483, is issued at the end of an FDA inspection when investigators think that they have observed conditions or practices that may violate federal law. It documents significant failures to maintain a sterile environment, including proper low humidity, appropriate temperature, and regular cleaning and disinfecting.

NECC said in a statement that it had received a copy of the report and would comment after reviewing it.

During an inspection on Oct. 2, after the steroid was recalled, the FDA found that 83 vials from one lot of the tainted steroid, shipped between Aug. 17 and Sept. 25, contained “greenish black foreign matter.’’ Another 17 vials from that lot of methylprednisolone acetate had white material floating in them. Further testing found that another 50 out of 50 vials from the same lot had “viable microbial growth,” the report found.

During a second inspection two days later, inspectors found numerous places where critical sterilization equipment had “tarnished discoloration,” “greenish yellow discoloration,” and yellow and green residue. Three locations were in or near autoclaves, used in the final sterilization of products intended for injection such as the steroid linked to the outbreak, methylprednisolone acetate.

In a teleconference with reporters, FDA officials declined to characterize the findings. They also declined to answer questions about whether an FDA inspection in 2004-2005 found similar conditions.

The extensive contamination and problems with sterile processing documented in the FDA report go beyond what Massachusetts officials had described in a report Tuesday.

“This reinforces the fact that this facility was just horrific,” said Eric Kastango, a consultant who works with compounding pharmacies on quality control and read the reports. “The amount of the microorganisms in the clean room was out of control and were red flags that someone could have acted on to prevent these contamination events.”

Sarah Sellers, a former FDA official who is now a consultant on quality and sterility issues, also reviewed the report. “The entire pharmacy was an incubator for bacteria and fungus,” she said. “The pharmacy knew about the contamination and did nothing.”

The report said personnel told investigators the company shut off the air conditioning each night from 8 p.m. to 5:30 a.m., a practice that experts said would make it difficult for the pharmacy to maintain a steady temperature.

“How hot did that room get?” Kastango said. “That becomes like a giant incubator for things to thrive. You never shut down the air conditioning in the clean room.”