Conservative critics have long doubted the impact, and in some cases the existence, of climate change.
But the agency said Wednesday that it had seen enough evidence with public transportation systems.
"Four of the nation's seven largest public transit systems are located in the northeast where climate change models forecast the largest increase in rain intensity in coming decades," the agency wrote. "In fact, the effects of a single storm touched one-third of the entire nation's transit riders."
The FTA added that there can be other problems with transit after storms as well.
"Rising sea levels pose an additional threat to transit agencies on our coasts," it said. "Besides flooding, severe precipitation can also cause landslides and mudslides. Extreme wind speeds can damage bridges, signs, overhead cables, and other tall structures."
The agency's blog post said that it was already working on some of the initiates other federal agencies have launched since the start of Obama's initiative.
"President Obama's climate change plan asks federal agencies to support climate-resilient investments and to help communities prepare for change," the agency wrote. "At FTA, the first test-case for these investments is Hurricane Sandy."
The FTA said it has $5.7 billion to help public transportation agencies recover from Hurricane Sandy, and $1.3 billion of the money will be used to fortify transit systems against the possibility of similar future storms.