Nintendo president Staoru Iwata has issued a personal letter of apology on the company's Japanese website.
The letter, translated by Giant Bomb, explains that while all hardware eventually drops in price, the degree and timing of the 3DS price-cut is "unprecedented" in the history of the company.
"We are all too keenly aware that those of you who supported us by purchasing the 3DS in the beginning may feel betrayed and criticise this decision," the letter reads.
"If the software creators and those on the retail side are not confident that the Nintendo 3DS is a worthy successor to the DS and will achieve a similarly broad base, it will be impossible for the 3DS to gain popularity, acquire a wide range of software, and eventually create the product cycle necessary for everyone to be satisfied with the system."
Iwata has already accepted responsibility for the company's declining performance, taking a 50 percent pay-cut. Nintendo's directors and executives also reduced their salaries by 20 to 30 percent.
"Those customers who purchased the 3DS at the very beginning are extremely important to us," the letter continues. "We know that there is nothing we can do to completely make up for the feeling that you are being punished for buying the system early."
In a concilliatory gesture, Nintendo has introduced the "Ambassador Programme", which gives 3DS owners 20 free downloadable games from the Nintendo eShop.