Partners in Health, a Boston-based charity dedicated to improving health care for people in poor countries, signed on to the Ebola fight last fall with high ambitions.

Unlike Doctors Without Borders and other relief agencies that specialize in acute response to crises, Partners in Health pledged to support the deeply inadequate health systems in Sierra Leone and Liberia for the long haul. Its leaders also publicly criticized the low level of care provided to Ebola patients and promised that its treatment units would do better.

“Let’s have a medical moon shot,” the group’s co-founder, Dr. Paul Farmer, said last October.

But the medical group, which had never responded to an Ebola outbreak before and had rarely worked in emergencies, encountered serious challenges.

Now, a previously undisclosed inquiry by international health officials and interviews with employees and managers of the aid group describe a pattern of safety lapses at a government-run treatment center in Port Loko, Sierra Leone, where Partners in Health worked. Staff members at the charity also cited a confusing leadership structure at the site.