Vishakhapatnam is the headquarters of the Eastern Naval Command and a key navy base.
The official said nearly 60 percent of the trees at the base have been uprooted and almost all roads are blocked.
"The officers and men of the naval base at Vishakhapatnam are working to get the base back to its operational status at the earliest," the official said.
"Damage in the Naval Dockyard was minimised by the proactive and preventive measures undertaken by all concerned," he added.
The airfield at INS Dega, which is naval air station, was flooded and damage has been reported to almost all buildings.
"With sustained efforts, both runways have been made fit for flying operations," the official added.
Power supply at the base has been disrupted due to damage in transmission lines and communications have been severely affected.