Mylan has said it is properly classifying EpiPen under guidance issued by CMS two decades ago.
The company, which has not been formally accused of violating the False Claims Act, declined to comment on Evercore's analysis or the NAMD letter.
CMS acting administrator Andy Slavitt, in a letter to Sen. Ron Wyden, D-Ore., this week, said Mylan has misclassified EpiPen as a generic product, and thus is paying a rebate rate of just 13 percent.
Instead, the company should be paying a rate of at least 23.1 percent due from brand-name products under the Medicaid Drug Rebate Program, Slavitt said.
But the actual rate Mylan should be paying now, Slavitt wrote, could be higher still since the program requires drugmakers who hike their prices above the rate of inflation to pay rebates beyond the 23.1 percent minimum.
Mylan has raised EpiPen prices well beyond the inflation rate. Since 2007, when Mylan acquired EpiPen, the company has raised the price of the device more than 500 percent.
Slavitt's letter said Medicaid paid nearly $800 million for EpiPens from 2011 to 2015 after rebates were factored in. In 2015 alone, Medicaid spent $365 million on EpiPen before rebates, which was more than five times the amount that Medicaid spent on EpiPen before rebates in 2011.
CMS could not comment on how much the agency believes Mylan has shortchanged Medicaid on rebates, he said. Nor did his letter say when Mylan was first notified of the incorrect classification.
Raffat of Evercore noted that the inflation penalty under the rebate program can make the rebates equivalent of up to 100 percent of the average manufacturer's price for drugs that have aggressive price increases.
"In other words," a slide from the Evercore analysis said, "if EpiPen was NOT supposed to be a non-innovator [drug, as Slavitt says] its rebates would have been so high that [net] sales to Medicaid should have been minuscule."
The rebates paid are split between the federal government and the individual state's Medicaid agencies, which jointly run that health coverage program.
In its letter to congressional staff last month, the National Association of Medicaid Directors wrote, "If EpiPen is considered a generic for Medicaid rebate purposes but is not an actual generic product, it appears Mylan is taking advantage of the" Medicaid Drug Rebate Program.
"At this time, there is not a readily available estimate of the total cost implications of this inconsistency in classification for EpiPen," the NAMD wrote. "However, a preliminary estimate from one state Medicaid agency indicates states are receiving only 15 percent of the quarterly rebate on EpiPen expenditures that they would otherwise be entitled to under the law if EpiPen were classified as a brand product."
The NAMD, which has not yet returned a call from CNBC seeking comment, did not identify the state agency in that letter. The letter was dated Sept. 8, but only posted online Monday, according to the group's website.
Mylan shares fell 2.4 percent to $35.94 on Friday.