The Chicago aerospace giant was assessed $5.4 million for what the agency said was failure to meet its obligations under a 2015 settlement.
Under that 2015 agreement, Boeing had said it would change its internal processes to improve and prioritize regulatory compliance.
Boeing "missed some of its Improvement targets" and "some company managers did not sufficiently prioritize compliance with FAA regulations," the agency said in a statement.
The company earlier had paid $12 million of civil penalties as an initial condition of the 2015 agreement.
To settle two other enforcement cases with the agency, Boeing will pay $1.2 million.
The FAA, which is part of the Department of Transportation, had originally proposed the two penalties back in August. The agency alleged at the time that Boeing managers unduly pressured or interfered with the work of FAA designated staff at the company's plant in South Carolina.
At last check Boeing shares were trading off 0.3% at $215.80. They closed the regular Thursday trading session down 5.6% at $216.45.