ANA Flight 1182 was en route to Toyama airport in central Japan on Saturday but had to return to the New Chitose airport for repairs, the airline said.
There were no reports of injuries among the 65 people on board.
The crack was found on one of the cockpit windows and the cause is under investigation, according to local media reports.
A plug covering a spot left for an emergency door tore off an Alaska Airlines plane as it flew 4,800 metres above Oregon on January 5, leaving a hole in the plane.
The FAA notified Boeing of the investigation in a letter dated last Wednesday.
“This incident should have never happened and it cannot happen again,” the FAA said in a statement.
Alaska and United Airlines reported finding loose bolts on door plugs that they inspected in some of their other Max 9 jets.
The FAA asked Boeing to respond within 10 business days and tell the agency “the root cause” of the problem with the door plug and steps the company is taking to prevent a recurrence.