Bosses have acted the day after Scottish poultry farmers were warned to keep birds indoors as a precaution against the highly-infectious avian flu.
The Royal Zoological Society of Scotland, which runs the attraction, said it had suspended the daily penguin parade - which dates back to 1951 - as a precautionary measure following the Scottish Governments announcement of an Avian Influenza Prevention Zone.
However visitors will still be able to see them from outside their enclosure and in underwater viewing areas at the zoo, which boasts the largest outdoor penguin pool in Europe.
A spokeswoman for the RZSS said: “Following the Scottish Government’s announcement of an Avian Influenza Prevention Zone in Scotland, we have taken the precaution of closing all walk-through aviaries until the restrictions are lifted.
“We have also temporarily suspended the penguin parade and have put in place increased biosecurity measures in line with Scottish Government recommendations.
"Animal welfare is our number one concern and we will always take precautions to minimise risk to our animals.
“The penguins will still be available to view during this time from outside the enclosure and underwater viewing areas.”