"We strongly recommend that all Pokémon X and Pokémon Y players download and install this update data," Nintendo said in a statement. "We apologize for the inconvenience."
Nintendo said the update prevents the occurrence of a "rare" issue where players are unable to resume playing after saving their game in certain areas of Lumiose City.
Those already affected by the issue will be able to resume playing after downloading and installing the update, Nintendo said.
The Pokémon X/Y update also promises to prevent errors that "sometimes" occur when using certain functions of the Global Trade Station (GTS), Nintendo said.
Pokémon X/Y launched worldwide earlier this month, selling over four million copies in its first weekend on sale.