Ransomware interrupted cameras, door-access control systems and critical monitoring systems at the site.
Officials said they believed the ransomware was sent in a malicious email link, clicked by an employee.
The US Coast Guard (USCG) issued a security bulletin on 16 December, urging other bases to take measures to prevent further attacks.
"Once the embedded malicious link in the email was clicked by an employee, the ransomware allowed for a threat actor to access significant enterprise information technology (IT) network files, and encrypt them, preventing the facility's access to critical files," it said.
"The virus further burrowed into the industrial control systems that monitor and control cargo transfer and encrypted files critical to process operations."