Staffers from the Justice Department have reportedly told both carriers that the deal may not be approved under its current structure, the Journal reported, citing people familiar with the matter.
Reuters later confirmed the report with one person familiar with the matter, who cautioned that a final decision has not been made.
Shares of Sprint plunged as much as 12% in after-hours trading following the report, while T-Mobile fell more than 4%.
A spokesman for Sprint declined to comment to CNBC. The Justice Department did not immediately respond to a request for comment.
About a year ago, T-Mobile and Sprint announced they had reached an all-stock deal to combine the companies. Shareholders of both companies approved the deal in October, which later received national security clearance.
Shares of Verizon slipped about 1% in postmarket trading Tuesday, while AT&T edged 0.6% lower.
Both Sprint and T-Mobile have argued that the merger is necessary to compete with the two larger carriers. The companies also said the merger will help Sprint and T-Mobile provide greater access to 5G.
Critics of the merger have argued it would lead to job loss, decreased competition and increased prices for consumers, especially in rural America.
In February, T-Mobile CEO John Legere defended the deal before Congress, asserting that the deal would create jobs and lower prices.