Warren's scathing letter comes on the heels of a similar complaint about the settlement made earlier this week by her fellow Democratic senator Richard Blumenthal of Connecticut, who called on the Justice Department to reject the deal.
Mylan declined to comment on Warren's letter. The company has previously said it was working with the Justice Department to finalize the settlement.
The Justice Department did not immediately respond to a request for comment.
Mylan has been under heavy public criticism since August, when outrage exploded over the company having hiked the price of EpiPens by more than 500 percent in recent years.
A two-pack of the auto-injector EpiPens, which are used to counteract the potentially fatal allergic reaction anaphylaxis, now costs more than $600. Many people with allergies or their parents feel they need to buy multiple packs of EpiPens, every year or so, to have in several locations, such as home, school, office and car.
Mylan, in response, has increased the level of financial assistance available to many consumers. It also plans on selling a generic version of EpiPen for about $300.
But increased attention on the company raised questions about whether it was paying the nation's Medicaid system, which covers primarily poor people, the correct rebates for EpiPens.
Under the rebate program, sellers of generic drugs pay 13 percent of their sales through Medicaid back to Medicaid, which in turn splits that money with the federal and state governments that jointly run it.
But sellers of brand-name drugs have to pay a rebate rate of 23.1 percent. And the rebates for brand-name drugs are even higher than that — sometimes much higher than that — if their sellers have raised the prices beyond the rate of inflation.
An analysis has found that if Mylan was paying the brand-name rebates, last year it would have rebated Medicaid nearly all the money it made in sales through Medicaid because of the inflation-adjustment enhancement.
Mylan for weeks had claimed it was paying the correct rebates, citing guidance previously issued for EpiPens by CMS.
But shortly after CMS chief Slavitt came out publicly and said the company had been told otherwise, the company reached a surprised settlement agreement with the Justice Department, without admitting any wrongdoing. As part of that deal, the company agreed to pay the higher rate for brand-name drugs starting next April 1. But neither Mylan nor the Justice Department has disclosed what rebate rate it will pay.
The settlement doesn't resolve all rebate-related issues for Mylan.
The company has disclosed it is being investigated by the Securities and Exchange Commission in connection with the rebates.
And there are questions about whether Justice's settlement with Mylan would preclude individual states from pursuing their own rebate-related legal actions against the company.
In a recent blog post, attorneys Ellyn Sternfield and Rodney Whitlock of Mintz Levin wrote that the Justice Department "does not have the authority to settle states' individual drug rebate claims against Mylan, which means any potential 'global' settlement with the states raises a variety of issues."
Those issues include the fact "Medicaid Drug Rebate settlement terms for each individual state will have to be agreed to by each individual participating state's Attorney General and in many states, also by the State Medicaid Agency," the lawyers wrote.