The world's biggest mobile phone maker had planned to release the Galaxy S5 - first unveiled in February - globally on April 11.
But the South's top operator SK Telecom, along with smaller rivals KT and LG Uplus, started selling the phone on Thursday.
Seoul's telecoms regulators have suspended all three firms from signing up new customers for 45-day periods each - ranging from March to May - as a penalty for offering illegal discounts.
SK Telecom's business suspension begins April 5 - before Samsung's planned Galaxy S5 launch date - and continues until May 19.
Samsung said in a statement that the earlier-than-scheduled release was made "independently" without its consent.
"We express our regret at this decision and we are working to verify all the facts," it said, adding it would stick to the April 11 release date for the rest of the world.
SK Telecom said the early release was motivated by a desire to "meet customer needs more quickly". It declined to elaborate further.
Samsung is hoping the Galaxy S5 will cement its lead in the global smartphone market.
The South Korean giant made about 30 percent of all smartphones sold in the world last year, nearly twice the share of arch-rival Apple.
The Galaxy S5 boasts a range of new features including a fingerprint scanner and a built-in heart rate sensor.
But Samsung faces a daunting challenge to keep momentum in the increasingly competitive and saturated market.
Competition is fierce in South Korea's vibrant mobile market, where the number of subscribers exceeds the country's total population of 50 million as many use several handsets.Nearly 70 percent of the subscribers use smartphones - one of the highest penetration rates in the world.