The two companies are scheduled to meet Assistant Attorney General William Baer Friday to discuss "significant concerns" with the deal, reported trade publication MLex, citing unnamed sources.
The regulators' concerns are focused on whether the deal will limit consumer choices for Medicare Advantages health plans for the elderly, according to reports.
The Justice Department declined CNBC's request for comment on the report. A Humana spokesperson wasn't immediately available.
"We continue to cooperate with the Department of Justice on its review," an Aetna spokesman told CNBC.
"Meetings with Bill Baer are generally regarded as negative," said Ira Gorsky, an analyst at Elevation Securities, in a research note. "It may be interpreted as Aetna being unable to adequately address the staff's concerns at this point, which increases the chance of litigation."
This meeting with Baer comes two weeks after he met with rivals Anthem and Cigna about their merger plans. According to the MLex report, the DOJ's top antitrust regulator told the companies that he backed the staff's conclusion that the merger would reduce competition in the employer market, and that divestitures weren't likely to remedy those concerns. The report did not cite its source for the information.
Stifel analyst Thomas Carroll said it makes sense that Aetna and Humana are meeting with regulators, saying it is likely getting close to the end of the review process and it makes sense that they may have been asked about divestitures and are now negotiating what would be acceptable.
"The process to review Aetna-Humana is simple when compared to Anthem-Cigna," he said, explaining that their one area of overlap is Medicare. "It's primarily one product — Medicare Advantage and Medicare Part D. Market share data is readily available, so it should be much more objective."
While there has been greater concern that the Anthem-Cigna deal would be blocked, the reports cast some new worries about the Aetna-Cigna combination.
The DOJ process may be "at this binary point" where the insurance deals could be blocked, Gorsky said.
Aetna said a year ago that it planned to buy Humana for about $37 billion, in what would be the industry's largest deal ever. Recent media reports have speculated that Aetna was preparing to sell billions in assets to quiet antitrust concerns in markets where the two companies have overlap.
A proposed merger between insurers Anthem and Cigna is also under review by regulators.
Humana closed at $162.74 on Thursday. The stock has fallen nearly 9 this year.
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