The change of power in the House has thrust NPR into "turmoil," according to the former chief executive of the organization.
Vivian Schiller said NPR has been through a "very difficult" time in the past several months. That's in part because of "the change in majority in the House," she said.
"It's a very difficult time with an incredible amount of scrutiny in what we do," she said.
House Republicans have voted to defund NPR this year, but Senate Democrats and the White House have expressed strong support for public media.
The measure would be "defeated handily in the Senate," according to Schiller, but there could be some cuts.
Her remarks come after she stepped down from the NPR helm a month ago following two controversies.
In March, a video sting put together by a conservative group appeared to show an NPR executive dismissing any need for federal funding and deriding the Tea Party movement.
In October, NPR executives fired news analyst Juan Williams following remarks he made on Fox News about Muslims. NPR said his remarks were inconsistent with editorial practices. Williams is now a columnist for The Hill.
NPR was loudly criticized by Republicans on Capitol Hill in both cases, and Schiller hinted that the Williams episode could have been handled better.
"As the CEO of an organization, you're ultimately responsible for everything, and I understand the way the world works," she said. "Speed kills" is a key lesson from the Williams controversy, she said.
Rejecting the notion in the video sting — that federal funding is unneeded — Schiller reiterated her call for public funding of NPR.