The municipality was alerted to the power failure around 9am on Tuesday, spokesman Siyabulela Makunga said.
The cause of the power outage was not clear.
He said the supply of power to the pump station had not been stable in the past few days. The weather in the region could be playing a role in the outages, but he could not confirm this.
Fort Beaufort’s central business district, golf course, prison and provincial hospital were affected as well as Newtown, Hillside, Healdtown villages and Bofolo township areas, Makunga said.
He said water trucks had already been dispatched to affected communities.
“[The municipality] regrets any inconvenience caused by these undesired occurrences.”
There was currently no alternative power supply. The municipality was attending to the matter, Makunga said.