Owners have complained of a silent ad for Pepsi interrupting playback several times an hour.
A spokeswoman for Samsung said it was only aware of the glitch affecting customers in Australia at this time.
The fault comes days after the company faced controversy over the way its TVs made use of voice recordings.Australian subscribers to Foxtel's app are among those affected
"We are aware of a situation that has caused some smart TV users in Australia to experience programme interruption in the form of an advertisement," the spokeswoman said.
"This seems to be caused by an error, and we are currently conducting a full and thorough investigation into the cause as our top priority.
"This situation has so far been reported only in Australia. We would like to apologise for any inconvenience experienced by our customers."
Users of at least two smart TV apps have complained about the issue:Plex - media centre software that allows owners to stream video files stored on a hard disk to other equipment. In most cases, the user would not expect to see any ads at all when using this Foxtel Play - an app installed by default on Samsung's Australian TVs, which provides access to the pay TV network's channels, which have ads of their own
News site Ars Technica noted that Samsung and Yahoo had been working together on a way to show pop-up ads on Samsung's smart TVs and suggested that the software involved might be the cause of the fault.
Samsung's PR team is also dealing with a backlash prompted by fears that its smart TV sets might be "spying" on their watchers' conversations.
Several commentators compared the policy to the surveillance state depicted in George Orwell's novel 1984.Samsung says its remote controls send voice data to Nuance
Samsung has since clarified the situation, saying there are two microphones involved:One built into the TV set, which responds to pre-set commands, such as, "Turn the volume up," but does not store or transmit the user's words while doing so Another embedded in its remote control, which does send speech to a third-party service - currently the voice recognition specialist Nuance - to let the TV respond to complex commands, including requests for movie recommendations. In addition, it said, the commands could be collected and studied by Samsung itself
The South Korean company said it had now altered its privacy document to read: "Samsung will collect your interactive voice commands only when you make a specific search request to the Smart TV by clicking the activation button either on the remote control or on your screen and speaking into the microphone on the remote control.
"If you do not enable Voice Recognition, you will not be able to use interactive voice recognition features, although you may be able to control your TV using certain predefined voice commands."