Park So-yeon, chief executive of the organization Coexistence of Animal Rights on Earth, has been accused of euthanizing more than 200 homeless animals and of secretly burying a number of them between 2015 and last year.
Park is also suspected of embezzling money from CARE sponsors and keeping it for her personal use, buying, among other things, a plot of land.
In her first official remarks following the allegations, Park told reporters that she sincerely apologizes for euthanizing homeless animals.
She decided to carry out the euthanasia in secret because of her "lack of courage and fear, because it could cause a huge controversy."
However, she said, "I clearly state that euthanasia by CARE was humanitarian mercy killing, not a mass cull."
Park also said she will fully cooperate with an investigation into the allegations.
The allegations came to light when a CARE staff member recently came forward with the revelation in a local media outlet, claiming that Park had many of the animals put down, mostly without the consent of other staff.
CARE has admitted to having administered lethal drugs to the animals, but only to those that were too sick or wild to keep in the shelter.
The controversy has stirred public anger, since CARE had an image as an activist organization dedicated to protecting animal rights.
Its rescue work became highly publicized for carrying out operations at dog farms and saving the dogs from being slaughtered or raised for fighting. The media has dubbed Park "the Queen of Rescues." (Yonhap)