The regulator added that it will not allow the planemaker to self-certify the jets, and has notified Boeing about the decision.
FAA said it will only issue airworthiness certificates when it is confident "Boeing's quality control and manufacturing processes consistently produce 787s that meet FAA design standards."
Boeing said it "will continue to work transparently through (the FAA's) detailed and rigorous processes... We will continue to engage with the FAA to ensure we meet their expectations and all applicable requirements."
In May last year, Boeing suspended deliveries of 787 after the FAA objected the proposed inspection method of the company. Since then, deliveries have remained halted.
The FAA said it wants Boeing to ensure it "has a robust plan for the rework that it must perform on a large volume of new 787s in storage" and that "Boeing's delivery processes are stable."
Delayed delivery of Dreamliner was due to factory defects and regulatory difficulties. The company used $3.5 billion to compensate customers for the delays.
Chief Executive David Calhoun said Boeing is still working with federal air-safety regulators about the defects.
Boeing will "have to complete the rework on a large fleet of airplanes... There's no way to shortcut it ... I wish it could go faster," Calhoun said. "I can't accelerate it."