The games giant posted the health warning on the website devoted to the 3DS handheld.
It said specialists had warned of possible damage that could be caused by 3D games which present different images to the right and left eye.
Younger children should only play 2D versions of 3DS games, said Nintendo.
Parental controlThe 3DS, the successor to the hugely popular DS handheld, goes on sale in late February in Japan and in Europe and the US in March.
The new handheld has two screens like older versions of the console with the top screen being able to show 3D images without the need for special glasses.
Parents should turn off this function if the handheld is going to be used by a child under six years of age, said Nintendo. It said the advice it had received from experts also applied to other 3D content that younger children might be exposed to.
In issuing the warning, Nintendo joins Sony and Toshiba in alerting people to the ill effects that can attend watching 3D movies or playing 3D games.
Sony has already said that parents should get medical advice before letting children watch 3D content on the PlayStation. Toshiba has said parents should keep an eye on children watching its TVs that can display 3D images without needing glasses.
The companies have also warned that watching too much 3D content can cause adults discomfort.