The company issued its first apology in a long-running dispute and withdrew from a legal bid to avoid paying out.
It brings the conflict one step closer to resolution only a month after talks appeared to have stalled.
But Samsung's chief executive Kwon Oh-hyun stopped short of admitting a direct link between working at the firm and developing leukaemia.
Mr Kwon said: "Several workers at our production facilities suffered from leukaemia and other incurable diseases, which also led to some deaths.
"We should have settled the issue earlier, and we are deeply heartbroken that we failed to do so and express our deep apology."
At a press conference, he said Samsung hoped to "resolve the issue with sincerity and earnestness". In a statement, he added: "We will make due compensation to the victims and the families."
An independent adjudicator would be set up in order to decide how to deal with each case with fairness and objectivity, with consent from the victims and the families, and Samsung would follow the compensation guidelines determined by it, Kwon said.
The world's top chip and smartphone maker did not say how many people might be compensated. But, according to Agence France-Presse, about 40 employees have filed claims with the state Korean Workers' Compensation and Welfare Service in the past six years.
