The error was discovered only when the heating system was shut down for the installation of a district heating system.
"As the coffee is black and the radiator water is a bit brown, then we haven't noticed the difference," said Captain Catharina Bergsell, information officer at the F 17 squadron.
She had however noticed that the coffee from the machine in the room where she works hadn't tasted that good.
"When you drink coffee from a vending machine it always tastes a little different than fresh coffee and it may not have the best consistency. An espresso machine has one flavour and coffee from regular coffee beans has another."
The problem has been that the coffee machine was connected to the heating unit, a closed system which pumps around 200-300 litres of water between the radiators, instead of the drinking water.
The radiators simply refilled automatically as staff continued to drink the heating system water.
It remains unclear why the machine was connected to the heating system and the matter will be investigated. Had the radiator not been switched off, the problem would most likely not have come to light.
"No one had a clue about this until the water was turned off. Had that not happened, I reckon it would not have been noticed until there had been a change of supplier or some such," Catharina Bergsell said.
The water in a closed system is usually considered bacteria free but it may still contain traces of metals, particularly iron but also lead, copper and manganese.
Staff at the air force base will therefore undergo tests, but there have been to date no reports of personnel falling ill.
A report has been filed with the Work Environment Authority (Arbestmiljöverket).