Despite the worrying findings, health officials said the likelihood of anyone becoming sick from eating the meat was low.
"It's unlikely that you would become infected through meat but it is unpleasant to know that there are resistant bacteria in the food that you buy," said Olov Aspevall, chief physician at the Swedish Public Health Agency.
The National Veterinary Institute, in conjunction with newspaper Dagens Nyheter, carryied out the review by sampling 20 packets of German and 20 packets of Danish pork purchased at stores throughout the capital.
In all, five packets contained traces of the bacteria, four from Danmark and one from Germany.
Although Swedish pigs do not currently have MRSA, the veterinary institute's Björn Bengtsson believes it is only a matter of time before they get it.