CMS Administrator Marilyn Tavenner added that new fraud-reporting requirements could potentially burden private business.
The HHS report singled out several areas of the country where pharmacies irregularly billed Medicare with extremely high amounts per beneficiary.
One such region was Miami, where nearly one in five pharmacies had questionable billings in 2009.
In Los Angeles, meanwhile, more than half of pharmacies with questionable billing charged for unusually high percentages of brand-name drugs.
The report cited arthritis medication Celebrex, which showed up three times more frequently in Los Angeles-area Medicare billings than in those from U.S. pharmacies generally.
Other areas, such as Detroit, Baltimore and Tampa, were most likely to submit suspicious charges involving controlled substances like prescription painkillers.
The National Community Pharmacists Association (NCPA) noted that the Medicare billings of "approximately 96 percent" of pharmacies were not found to be problematic.
A statement from the group added that for the other roughly 4 percent, the HHS report lacked "sufficient detail to evaluate the medical legitimacy and appropriateness of the claims."
"Community pharmacists look forward to continuing to work with Medicare, Congress and health plans on appropriate steps to protect against fraud," the statement read.
Federal investigators urge stronger oversight of Medicare Part D
By Elise Viebeck - 05/10/12 09:03 PM EDT