According to a draft report leaked to reporters, some in the agency believe the health benefits of fish far outweigh the risks, and that people should eat more fish, even if it contains mercury.
The report argues that nutrients in fish could raise a child's IQ by 3 points.
But the report has is said to have alarmed scientists at the Environmental Protection Agency.
The new guidelines were developed and vetted by FDA staffers, and the draft report was sent to the White House Office of Management and Budget.
A spokesperson for the FDA says the agency intends to seek comment from the public.
This afternoon, the agency issued a statement saying, "It would be a mistake to assume that this draft report represents the FDA's official position because a final determination on these matters has not been reached."
But environmental critics say the fact the report was already in White House hands indicates the decision was made.