Almost half of the 2.2 million troops deployed in Iraq and Afghanistan report difficulties on their return home, but many receive inadequate care from the US Department of Defense and Veterans Affairs, according to a new study published on Tuesday.

The Institute of Medicine report, requested by Congress and funded by the Pentagon, expressed "serious misgivings" about methods used to treat the "significant numbers" of returning veterans with post-traumatic stress disorder (PTSD), depression and substance use disorder. It cited tools and treatments used by the DOD which had "no clear scientific evidence base" and said more needed to be done to evaluate their effectiveness.

The study, aimed at examining lingering problems of veterans returning from both conflicts, also called into question a Defense Department policy which bans restricting access to private weapons "even if a service member is at risk from suicide".

It examined veteran suicides, high unemployment rates and also the ramifications of the "high rates" of military sexual assault, all issues that have attracted recent congressional attention.

George Rutherford, the report's co-author, said DOD had been slow to address the needs of returning veterans.

"Although several federal agencies are actively trying to address the support needs of current and former service members deployed to Iraq and Afghanistan as well as their families, the response has been slow and has not matched the magnitude of this population's requirements as many cope with a complex set of health, economic, and other challenges" said Rutherfold, chair of the IOM's committee on the assessment of readjustment needs of military personnel, veterans, and their families.

"The number of people affected, the influx of returning personnel as the conflicts wind down, and the potential long-term consequences of their service heighten the urgency of putting the appropriate knowledge and resources in place to make re-entry into post-deployment life as easy as possible."

The IOM, an independent nonprofit organisation, is part of the National Academy of Sciences.

Among its key conclusions, the report said:

• The DOD and the VA should do more to assess the efficacy and adequacy of treatment, especially if it is to be offered nationally. The tool used to assess cognitive function after a brain injury has "no clear scientific base" and the "Acceptance and Commitment" therapy used by the VA for depression "lacks sufficient scientific evidence to support its use as a first line intervention", it said.

• Research shows that restricting access to lethal weapons prevents suicides, but, the report found that, even if a service member is at risk for suicide, DOD policy prohibits restricting that individual's access to privately owned weapons. In 2010, half of all the 300 military suicides were by those who had deployed in the Iraq and Afghanistan conflicts, the report said. An estimated 22 veterans take their own lives every day, according to a VA report last month.

• It recommends that the DOD and VA "expand its definition of family" to include unmarried partners, same sex couples single parents and stepfamilies.

• It calls on the DOD and VA to work together "link and integrate" their databases to share data to track problems of personnel more effectively. A "large array" of relevant data, which could be used to answer key questions about re-adjustment, are being collected by several federal departments and agencies, the comprehensively analysed to answer many key questions about readjustment, the committee said.

• The DOD should make reducing domestic violence a priority, to combat the "troubling rise" in domestic violence in service members returning from deployment, "typically involving abuse of spouses or neglect of children".

The 500-plus page report found that 44% of troops returning from Iraq and Afghanistan reported difficulties. Up to one in five suffers from PTSD, while a similar number have mild traumatic brain injury (TBI), the report says. Some have overlapping health conditions, most commonly PTSD, substance use disorder, depression and symptoms related to mild TBI. It noted that the unemployment rate among veterans aged 18-24 was over 30%, compared to 16% for civilians.

This month, members of Congress sent a letter to the chiefs of DOD and VA seeking data to investigate a new theory linking TBI with the military's suicide crisis.

It warned that veterans' needs would take decades to peak, based on previous conflicts, highlighting the need to manage current problems and plan for future ones.

Tom Tarantino, chief policy officer of the Iraq and Afghanistan Veterans of America, which represents 200,000 people, said the IoM report was "spot on".

"It confirms a lot of things that our members are telling us on the ground," said Tarantino. "The majority of veterans don't have problems but the ones that do, the Department of Defense are just too slow to implement changes."

Citing the IOM's recommendation for the DoD and the VA to have linked databases, Tarantino said it was "astonishing and inexcusable" that it hadn't already happened.

In April 2009, President Obama promised a unified lifetime electronic health record for armed servicemen and women "from the day they first enlist to the day that they are laid to rest".

But four years later, said Tarantino, it still hasn't happened. The inability of the VA and the DoD to "electronically talk to each other" remains one of the biggest obstacles to getting quality of care, he said.

Asked about the DoD's use of treatment which had no scientific base, Tarantino quoted General George Patton, who said "a good plan violently executed now is better than a perfect plan next week".

"There is a lot we didn't know about these injuries. Even in 2013 we still don't know as much about PTSD that we should. It's critical that we move to evidence-based practice and have a clear way forward."