The upper echelons of the FDA are getting a lot of unwanted attention today. Yesterday, the top regulator of the medical devices division, Daniel Schultz, announced his resignation, and now the head of drug approvals is under investigation by the Department of Health and Human Services, reports the Wall Street Journal.

For months, the medical devices division has been on the list of Margaret Hamburg, whom Obama appointed to whip the controversy-plagued FDA into shape. At the center of the division’s current mess are products that were approved despite the safety and efficacy concerns of agency scientists. The approval of such products — including a brain-zapping depression-treating device and a knee surgery device — led to allegations of being a bit too friendly with industry.

The criticism isn’t just from outsiders. In a letter to the House Energy and Commerce Committee last October, nine employees alleged that some scientists had been pressured to approve the devices.

Schultz has some company. Janet Woodcock is the director of the FDA’s Center for Drug Evaluation and Research, which approves drugs, and is also accused of being too cozy with industry. (Back in November, she was a drug maker hopeful for FDA commissioner but didn’t get it).

Amphastar Pharmaceuticals has been trying to win approval for a generic version of the blood thinner Lovenox, which has generated billions of dollars for its maker, Sanofi-Aventis. Amphastar’s approval process has been going on for six years, during which the company alleges that Momenta Pharmaceuticals, who submitted an application for its own generic version of Lovenox two years after Amphastar, had “special access” to Woodcock at “critical times”.

While both companies were vying for approval, the Wall Street Journal says Woodcock asked Momenta founder Ram Sasisekharan to lead an FDA task force (to investigate tainted Chinese-made heparain).

“Drs. Woodcock and Sasisekharan, along with other Momenta scientists, then co-authored two medical journal articles last year identifying the cause of the contaminated Chinese heparin imports, a finding that won scientific — as well as Wall Street — kudos for Momenta”, noting that their stock jumped 17 percent in a day after the article was published.

Amphastar is asking that Woodcock “recuse herself from the entire matter”, says the WSJ.