Facebook and the FTC declined to comment.
All deals over $68.2 million trigger an automatic 30-day review. If regulators still have antitrust concerns, they then issue a second request for information.
Antitrust law prohibits any deal that would "substantially reduce" competition.
The Financial Times cited experts who said the Instagram purchase may have invited additional scrutiny because of the high price Facebook was willing to pay, indicating it may have been paying a premium to kill off a potential competitor.
The experts also said they expect that regulators will eventually approve the deal.
Facebook would owe Instagram $200 million if the deal collapses.