TOKYO — In a blow to the prestige of Japan’s scientific community, a government-backed research institute accepted the resignation of one of its highest-profile scientists on Friday after she failed to replicate research results that were once hailed as a breakthrough in stem cell research.

The institute, Riken, had given the researcher, Haruko Obokata, 31, three months to repeat the experiments that were the basis for her claimed discovery earlier this year of a remarkably simple way to make stem cells, a type of cell that could hold the key to futuristic medical treatments. On Friday, the institute announced that she had failed to replicate a new type of stem cell known as STAP cells, for stimulus-triggered acquisition of pluripotency, a term that refers to the cells’ ability to turn into any other type of cell.

That ability allows stem cells to grow into any kind of cell, like muscle and brain cells. By appearing to offer an easier way to make stem cells, Ms. Obokata’s claimed discovery of STAP cells seemed to bring doctors a step closer to medical treatments in which they could regenerate damaged nerves or other tissues or even grow entire organs.

However, at a news conference in Tokyo on Friday, Riken officials said they had concluded that there was little likelihood that such STAP cells actually exist. Bowing in apology, they also said they had accepted the resignation of Ms. Obokata, a stem cell biologist at the institute’s Center for Developmental Biology in Kobe.