Chief Guina Pig and the other guinea pigs are only in Operation: F.I.S.H.Y..
Numbuh 2 says that the guinea pigs were used before hamsters and found their way to the edges of the tree fort and have become primitive compared to hamsters. Guinea pigs are based on hunting tribes due to their clothing a deadly nature. However, the Guinea Pigs are also seen fighting with the cats which isn't shown and the only part of the battle is seconds before colliding. No other appearances of the Guinea Pigs have been confirmed.