Suggestion

Fui tradutor juramentado da Capitania dos Portos do Maranhão e o termo que usávamos (e que todos os outros juramentados usavam) era harbor master para quem cuidava da segurança da navegação.
O termo port authority era usado para ao responsável pelo porto em si. Por exemplo, No porto do Itaqui o port authority era a EMAP, no porto de Ponta da Madeira o port authority era a Vale, mas todos os navios estavam sujeitos às regras da capitania dos portos - harbor master.


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Note added at 11 hrs (2017-01-18 12:54:06 GMT)
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Frequently, harbormasters have police powers and act as head of the ***port police***. The main functions of such police are enforcement of the port bylaws, especially with respect to ***traffic regulations***, protection of the environment, and ***accident prevention***.

I have worked in liner shipping for donkey's years and by far the equivalent term most often found for "Capitania dos Portos" is the one I mentioned. I assume "Harbour Master" (Port Captain) is the British version.

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Note added at 2 days2 hrs (2017-01-20 03:50:25 GMT)
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By the way, Port Authority usually relates to the State Dock Company, rather than the Port Captaincy, which is directly associated with the NAVY for maritime accidents and seamanship.