The update, which reportedly weighs in at 5GB, can take over an hour to install, and multiple users have claimed that interrupting the process has rendered their consoles unusable.
One affected party, LA Times journalist Ben Fritz, says there's no warning not to turn off the system during the install and no cancel option.
He ran into problems after unplugging his Wii U while downloading the update, and says he has since been contacted by multiple users whose consoles were also bricked when their power or internet went down mid-install.
A support message on Nintendo's US website asks new users to be patient and not to turn off the console while updating it.
"The length of time it takes to perform a system update varies depending on the speed of the Internet connection used. Please be patient," it says.
"Due to the amount of new features and applications included, the system update may take an extended amount of time when performed during the initial setup (for some users it could take an hour or more to download and install). Do not power off your system during this time."
Nintendo has also confirmed an outage to Miiverse, Wii U's embedded social networking service, which commenced last night and remains ongoing.
"So many Miis have jumped on Miiverse that some may be having problems connecting to the service," the firm added on Twitter. "We are in the engine room getting it fixed!"
Nintendo's management of online security measures has come under scrutiny after it emerged this weekend that one Wii U buyer apparently hacked into the console's online platform just hours after getting the system. Nintendo has confirmed to CVG that the incident was not a hoax, though the corporation has played down the severity of the issue.
Earlier today it was also reported that Nintendo Network accounts are currently tied to a single Wii U console, which seemingly means players won't be able to transfer their account data to a new system should their original break or go missing, resulting in the loss of any stored game progress and digital purchases. We're awaiting clarification on this matter from Nintendo.