Military investigators responding to reports of sexual assaults do not always follow the widely accepted standards set by civilian police agencies, according to a new Pentagon Inspector General’s report.

The IG’s probe began almost three years ago, in November 2011, and focused on how sexual assault allegations are handled by the three military investigative agencies, the Army’s Criminal Investigation Command, known as CID, the Naval Criminal Investigative Service and the Air Force Office of Special Investigations.

The report comes after months of internal controversy over the final report. The service’s criminal investigations divisions leveled harsh criticism at the IG and prompted the IG to remove some elements from a draft version and scale back the scope of the final report, according to the report.

The final draft concluded that the military investigators adhere to most of the standards outlined by the International Association of Chiefs of Police. But the IG cited several exceptions, which included:

■ The Army’s CID and the Navy’s NCIS should consider changing their policies to encourage sexual assault investigators to proceed with a thorough investigation regardless of whether they obtain laboratory findings.

■ The NCIS should make sure that support personnel advise victims against bathing or urinating to ensure the potential for reliable laboratory samples.

■ The NCIS should clarify protocols for cases that involve a victim’s illegal substance abuse or underage drinking to ensure that the information is not used to discredit the victim or discourage reporting.

■ The Air Force’s OSI should advise investigators to “ask victims to explain what they remember and how they felt” during and after the assault.

■ The OSI should encourage investigators to routinely consider whether stalking charges apply in each case because surveillance behavior is a common precursor to sexual assaults.

■ The NCIS should create a timeline for inclusion in official reports to document the victim’s trauma or post-assault behavior, including weight gain or loss, changes in daily routines, etc.

■ The NCIS should advise investigators, in cases where a victim requests to have a support person such as a spouse or parent present during questioning, to look for signs of hesitation from the victim or signs of controlling or intimidating behavior by the support person.

The CID criticized the initial draft of the report completed in June, saying it “failed to meet the accuracy standard.”

The IG’s office acknowledged that “we revised the report as appropriate to ensure data accuracy, relevance, and objectivity.”

In one specific example, the initial draft called out NCIS for not adhering to an IACP’s recommendation to videotape victims’ statements. But NCIS said that misstated the IACP’s views on the subject. The IG removed that element from the report after checking with the IACP and determining that the civilian association “takes a more neutral view of videotaping victim interviews.”

In the final report, the IG dropped dozens of IACP-recommended actions from its evaluation of the military investigative agencies, reducing the total number of actions cited from 165 to 92, according to the report.

The complete report is at militarytimes.com/IG-sexual-assault.

Andrew Tilghman is the executive editor for Military Times. He is a former Military Times Pentagon reporter and served as a Middle East correspondent for the Stars and Stripes. Before covering the military, he worked as a reporter for the Houston Chronicle in Texas, the Albany Times Union in New York and The Associated Press in Milwaukee.