The firm failed to meet a deadline to provide fuel tank safety instructions to airlines, among other issues, the Federal Aviation Administration said.
Boeing has agreed to pay the fine and take action to improve certification.
The agency said it "does not allege that these issues created unsafe conditions".
"It is imperative that everyone complies with our aviation system's high safety standards," said US Transportation Secretary Anthony Foxx.
"This agreement is an important step toward ensuring that Boeing fully meets all applicable compliance standards going forward."
The other violations involve Boeing's delay in addressing incorrectly shaped fasteners used on airliners, as well as production quality control problems.
FAA administrator Michael Huerta said: "Boeing has agreed to implement improvements in its design, planning, production and maintenance planning processes, and has already implemented several of these improvements."
Aircraft maker Boeing is to pay a $12m (£8m) fine for "multiple pending and potential enforcement cases", the US air regulator has said.