Robert Weaver, an insurance broker and member of the Quapaw tribe in Oklahoma who was appointed in October, made the decision after the Journal reported he had exaggerated his career history. Those reports raised tough questions from members of the Senate Indian Affairs Committee.
Weaver's withdrawal leaves the IHS, a division of the Department of Health and Human Services (HHS) that provides care for federally recognized tribes in the U.S., without an immediate replacement. The post hasn't had a permanent leader since 2015.
Michael Weahkee, the current acting director for the agency, informed tribal leaders of Weaver's decision at a recent IHS panel discussion.
The agency has been struggling to provide health services to the nearly 2.2 million tribe members under its care, many of whom live in isolated rural regions.
Many hospitals and clinics run by the agency have faced decreased federal funding, leading to closures and the loss of vital services.
The recent HHS budget proposal would provide $6.8 billion for the IHS in fiscal 2019, adding $513 million.
Native Americans have also been among the hardest hit by the opioid epidemic, with overdose rates rising by 500 percent from 1999 to 2015, according to the CDC.
This story was updated at 5:14 p.m.