Although the FCC allowed AT&T to withdraw its application, the agency decided to release its analysis of the deal anyway.
In a damning 109-page report, FCC staff conclude AT&T did not prove their deal would benefit the public.
They write that the merger of the second and fourth largest wireless firms would reduce competition throughout the country's major markets and would lead to massive layoffs.
AT&T accused the FCC analysts of cherry-picking facts and questioned whether they had made up their minds before reviewing the data.
In the letter, the lawmakers also asked Genachowki about the report's use of the "spectrum screen," a test to determine whether the transfer of wireless licenses could harm competition.
"The FCC apparently changed its spectrum screen in the recently released staff analysis on the AT&T / T-Mobile transaction, a document that was not adopted by the FCC," Upton and Walden wrote. "Moreover, questions remain as to how the Commission uses the spectrum screen."
An FCC official said the agency updated its screen to reflect changes in the spectrum available for mobile broadband use.