An Interior Department watchdog report released earlier this month that was intended to quiet allegations of scientific misconduct in evaluating the noise impacts of Drake’s Bay Oyster Company instead unleashed more cacophony this week.

Corey Goodman, the scientist and biotechnology entrepreneur friendly to the oyster farm who wrote a complaint that spurred the investigation, said Monday that the report deflected several of his allegations and invented others. An examination by the Point Reyes Light found that the report appears to downplay evidence contradicting its conclusions and in at least two cases is factually inaccurate.

“I see two separate issues going on here: one issue has to do with a family business and 31 workers losing their jobs, losing housing, California losing a major source of oysters,” Dr. Goodman said. “Bigger and broader is how do we use science in the federal government and how do we use science in our actions.”

Dr. Goodman’s challenge of the report—the second investigation by that office into allegations of federal misconduct against Drake’s Bay—turns a spotlight on the Acting Inspector General for the United Sates Department of the Interior, Mary Kendall, who has faced criticism from congressional Republicans, environmental groups and a small but growing number of her own employees.

While Ms. Kendall has been praised by some in Washington, the former Environmental Protection Agency lawyer is currently under investigation by the House Natural Resources Committee for a conflict of interest in reviewing whether the White House improperly edited a report to inaccurately suggest that experts supported a moratorium on oil drilling in the Gulf Coast after the BP oil spill.

Nearly sixty percent of Interior employees said the Inspector General was “free from improper influence” from the department, a declining number from past years, and nearly 15 percent said the office was not free from influence. Ms. Kendall has denied wrongdoing. Kris Kolesnik, the associate inspector general for external affairs, did not return a call seeking comment.

The environmental whistleblower protection group Public Employees for Environmental Responsibility (PEER) has been repeatedly critical of Ms. Kendall’s four-year tenure, which started after the release of the first report examining allegations of misconduct and was critical of federal scientists.

“There have been increasing criticisms from within the [Office of the Inspector General] that the Inspector General has been trying to curry favor with the Interior Department, which is in direct conflict with being a watchdog,” PEER Executive Director Jeff Ruch said, describing the leadership in the office as being at a “low point.” “A decent Inspector General who actually followed up on leads would be a good thing.”

In 2011 Mr. Ruch’s group occasionally supported National Park Service scientists who found deleterious environmental impacts from Drake’s Bay Oyster Company. “We thought the scientific issues were completely irrelevant to the decision” by Interior Secretary Ken Salazar, Mr. Ruch said.

West Marin Environmental Action Committee Board President Bridger Mitchell said he was pleased with the Interior investigation. “It’s a very thorough report,” he said. “It responded point by point to each of the allegations that were made in Mr. Goodman’s complaint and it found no basis for any of those allegations.”

The Interior report said that investigators “found no evidence” of deviation from National Park Service (NPS) policies by using “proxy” data or that there were any early indications of soundscape issues. But NPS regulations cited by Dr. Goodman state that, “The Service will strive to preserve or restore the natural quiet and natural sounds associated with the physical and biological resources of parks. To do this, superintendents will carefully evaluate and manage how, when, and where motorized equipment is used by all who operate equipment in the parks, including park staff. Uses and impacts associated with the use of motorized equipment will be addressed in park planning processes.”

Mr. Mitchell said he was not sufficiently aware of government regulations to comment on whether NPS officials violated their own policies, but he said government agencies were not in a position to take measurements for “every landscape that they’re charged to make a report on.”

Ultimately, he said, it was not necessary to have an Environmental Impact Statement to deal with citizens’ concerns about the oyster farm. “It would certainly be helpful if people who are making charges of bias and fraud would just refrain from that type of inflammatory and non-objective kind of commentary and look hard at the evidence that is there.”

For Mr. Mitchell, evidence of Drake’s Bay’s noise impacts comes from personal experience. “I go there to have tranquility and the opportunity to just enjoy the outdoors in a very special place,” he said. “The impact of the sounds one time when I was boating there was very loud radios and motorized equipment happening. It took quite a few minutes of paddling to get where it was no longer audible, fairly deep into the estero.”

The whine of a motorboat could be perceived for several minutes, even in the distance, when the motorboat could only be seen through binoculars, he said.

The Interior report also appears to ignore evidence that Chris Clark, a Cornell University professor who peer-reviewed the document, originally believed he was reviewing noise measurements from Drake’s Bay when in fact he was reviewing proxy data.

While he is named only as “the peer reviewer” in the report, Dr. Clark is quoted as saying “he knew some of the actual data… were representative or proxy data…” The comments conflict with what Dr. Clark told a reporter with Greenwire last year. Dr. Clark did not respond to several requests for comment.

Some quotes attributed in the report to Dr. Goodman do not appear in a copy of his complaint, and Dr. Goodman said he has never written those words. The Inspector General’s report said that Mr. Goodman accused [NPS staff] of failing “to recuse themselves” from the Environmental Impact Statement process “despite the appearance of conflicts of interest,” and that the NPS influenced their contractor to report “unfavorable findings.”

While Dr. Goodman’s complaint is critical of NPS officials, and he does say that NPS should not be involved in investigating themselves, he does not make an argument that they should have recused themselves. And while he invites investigators “to probe the original goals of the… soundscape analysis” and microphone placement, he did not describe undue influence by NPS officials on their contractor.

The Interior report said they found no evidence that NPS interfered with or influenced their contractor’s reports.

The report incorrectly states that the Environmental Impact Statement found that “socioeconomic” factors instead of “wilderness” would be majorly impacted by continued oyster farming. In fact, the socioeconomic impacts were found to be “minor” and the wilderness impacts were found to be “major.”

Dr. Goodman also disputed the report’s characterization of his views on the Environmental Impact Statement, paraphrasing him as saying that the impact statement was “unwarranted and therefore wasted taxpayer funds.” Dr. Goodman said he has never made such a statement and does not agree with it. His original complaint does include the statement, “The allegations contained in this complaint involve fraud and ultimately the abuse and waste of taxpayer money.”

Dr. Goodman said, “I never spoke out against [the] process for looking at environmental impacts, which is the way they try to misquote me. Rather I said that the way in which NPS went about this [Environmental Impact Statement] process, and the six-year saga of looking for negative adverse environmental impacts where none had been found … wasted taxpayer money.”