In a statement, Jindal praised Greenstein's tenure at the health department, during which he oversaw the privatization of many state-run health facilities and shifted much of the Medicaid program to private managed care.
"Bruce has successfully led one of the largest transformations of our state's health care delivery system," Jindal said.
Greenstein started work at DHH in September 2010.
Before taking the helm of Louisiana's largest state agency, he was a health economist and managing director of worldwide health for Microsoft Corp. Other past jobs included work for the federal Centers for Medicare and Medicaid Services and health policy analysis for the Government Accountability Office, Congress' investigative arm.
When Greenstein leaves, his deputy secretary, Kathy Kliebert, will serve as interim secretary of the department and will receive the same annual salary Greenstein was paid, according to Jindal's office.
Greenstein hadn't been seen at public events since news of the Baton Rouge-based federal grand jury probe. Lawmakers were irritated that the health secretary skipped his agency's budget hearing earlier this week.
On Friday, a DHH spokeswoman referred all questions about Greenstein's resignation to the governor's office.
CNSI, which was supposed to take over the Medicaid work next year, is challenging the termination of its contract by the state. CNSI beat three other companies for the work, but critics said the company underestimated the true cost of the job and made incorrect assumptions to win the bid.
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