"The public's interests would be gravely disserved by acceding to plaintiffs' premature efforts to take down the entirety of the negotiation program — which achieves a longstanding goal of controlling skyrocketing Medicare spending and making drugs more affordable for seniors — before that program even begins," the Justice Department said.

However, the Chamber of Commerce is only one of several organizations, along with the trade group PhRMA, Merck, Bristol Myers Squibb and Johnson & Johnson, suing the U.S. Department of Health and Human Services over the negotiation program. The DOJ argued that these suits "should have an opportunity to proceed on their own schedules, without interference from this case." The department added these recent lawsuits were an attempt to accomplish what lobbying could not.

Related: Merck sues HHS and CMS, calling plan to negotiate drug prices 'extortion'

"Drug manufacturers lobbied hard against legislative efforts to seat the secretary at the negotiating table," it said. "And now that their lobbying failed, manufacturers and interest groups have run to court, filing multiple suits around the country challenging the statute on its face."

The Justice Department questioned the chamber's standing to sue over the program. Although the organization is not a pharmaceutical company or trade group that represents that industry, the chamber has said it is suing on behalf of its members that are drugmakers and previously has said there is precedent for it to file such a lawsuit.

The Centers for Medicare & Medicaid Services is set to announce the first 10 drugs eligible for negotiation by September 1. After that, the manufacturers of these drugs will have one month to sign agreements to participate in the negotiations.