BOSTON (Reuters) - The U.S. Food and Drug Administration took 684 days to issue a warning letter after uncovering serious issues at the pharmacy at the center of the deadly U.S. meningitis outbreak, newly released documents showed.

The New England Compounding Center (NECC) chastised the FDA for taking so long, telling the agency its response time was nearly 18 months longer than the FDA's average response, according to letters released by a Freedom of Information Act request from Reuters.

Since the FDA's December 2006 warning letter to NECC, both sides have come under intense scrutiny. State and federal regulators, including the FDA, are being asked why they didn't move sooner against NECC, given a long history of concerns about the family-owned pharmacy's operations.

The Centers for Disease Control and Prevention said 34 people have died and 490 have been injured after Framingham, Massachusetts-based NECC shipped thousands of fungus-tainted vials of methylprednisolone acetate to medical facilities throughout the United States. The steroid was typically used to ease back pain.

On Tuesday, defense lawyers for NECC's owners told a U.S. District Judge in Boston there was nothing to show they had a direct hand in the cause of the meningitis outbreak.

But the newly released documents reveal a combative side to NECC chief pharmacist, Barry Cadden, and his brother-in-law, Greg Conigliaro, the recycling entrepreneur who helped him launch the specialty pharmacy.

Inspectors said Conigliaro became indignant during a September 2004 inspection by the FDA and Massachusetts regulators, documents showed. At one point, Cadden told his brother-in-law, "Don't answer any more questions!" according to a 2005 FDA memorandum.

The inspectors had concerns about how NECC was compounding and dispensing Trypan Blue, a dye sometimes used in eye surgery. Inspectors also expressed concern about how NECC was repackaging Avastin, highlighting the threat of contamination when the pharmacy opened sterile containers of the cancer drug.

The FDA's eventual warning letter to NECC in December 2006 was based on an inspection that began in September 2004 and ended on January 19, 2005, according to the documents.

"This prolonged gap between inspection and warning letters does not comply with FDA's procedures," Cadden, NECC's chief pharmacist, wrote in a January 5, 2007 letter to FDA compliance officer Ann Simoneau.

In follow-up correspondence, FDA officials apologized for the "significant delay" in correspondence time between the inspection and the warning letter. While the FDA conceded the gap was unusual, it in no way diminished the regulator's "serious concerns" about NECC's pharmacy operations, documents showed.

(Reporting by Tim McLaughlin; Editing by Jeffrey Benkoe)