“We are doing everything we can to advance congestion pricing,” Patrick J. Foye, the M.T.A. chairman, said in an interview. For the process “to be held up by what I’ll call a cynical use of the environmental review process is just wrong,” he added.

M.T.A. officials met or spoke with federal authorities about congestion pricing on at least 13 occasions between April and December last year, according to Kenneth Lovett, a senior adviser at the M.T.A.

New York’s congestion pricing plan requires federal approval because some roads within the designated congestion zone in Manhattan have used federal aid for construction.

Tolls are not generally allowed on such federally assisted roads, though the federal government has approved tolls for some roads and highways around the country to reduce congestion and pay for road construction.

On Thursday, Mr. Cuomo met with Mr. Trump to discuss the decision to end New Yorkers’ access to the Trusted Traveler programs. But the meeting sparked fresh tension, with both men attacking each other in interviews or on Twitter afterward.

Mr. Trump has not indicated whether he will personally intervene in the Federal Highway Administration’s approval process or whether the two men discussed it during their meeting last week. It remains unclear how the president feels about congestion pricing and neither supporters nor opponents of the plan could recall Mr. Trump ever saying anything on Twitter or speaking publicly about it.

Some transportation advocates have questioned whether Mr. Cuomo is using tension with the White House as an excuse to slow down the rollout of congestion pricing. The state law approving the plan specifies that it can begin no earlier than next January, but does not mandate that it be put in place by then.