The move will allow customers to purchase products for both systems with a single eShop profile, similar to Sony's Entertainment Network system.
"A unified account system will be implemented later this year with the launch of the Wii U. Eventually this same account system will be made compatible with Nintendo 3DS systems," Nintendo customer service rep David Marshall told Nintendo World Report.
"At this time we have no additional details to offer and nothing to indicate how or if this will work outside the United States and Canada."
Nintendo has previously required users to sign up for separate accounts to purchase digital software for its Wii, DSi and 3DS platforms.
The Wii U is expected to be released in time for the Christmas season, though a specific launch date has not been set.
Watch Digital Spy go hands-on with the Wii U below: