The director of the Veterans Affairs Montana Health Care System has resigned as the agency conducts an internal investigation into allegations of senior leadership misconduct.

John Ginnity, who has led the state VA’s medical system since March 2015, announced his decision to leave in a letter Wednesday to staffers at Helena’s Fort Harrison Medical Center.

Ginnity submitted his letter of resignation on Tuesday. His last day on the job will be July 8.

“While there are several factors contributing to my resignation, my family and health are my main priorities at this time, and as such we have made this decision after several months of consideration,” Ginnity wrote in his letter to staffers. “I will continue to support veterans as I have done faithfully for over 25 years of service through other opportunities.”

U.S. Sen. Steve Daines’ office released a letter Wednesday from Veterans Affairs Undersecretary for Health David Shulkin that said the agency is investigating allegations of senior leadership misconduct at Fort Harrison. The letter does not say that Ginnity was a subject of the investigation.

Ginnity was named the permanent Montana VA director in February 2015 as the agency faced pressure from the Montana congressional delegation for months to fill the position.

The system had been without a permanent director since June 2014.

With Ginnity’s resignation, people in the top three leadership positions at VA Montana will be operating in an “acting” capacity, according to a news release from U.S. Sen. Jon Tester, D-Mont.

In a statement, the VA estimated it could take 90 to 120 days before the VA is able to fill Ginnity’s position.

A Montana VA official said an acting director will assume the director duties in July. Interim assignments usually last 100 to 120 days at a time.

The VA is experiencing a 45 percent vacancy rate among senior executives nationwide, according to the statement. In Montana alone, the associate director position has been vacant more than two years. The chief of staff position has been vacant for nearly a year.

U.S. Rep. Ryan Zinke, R-Mont., said Veterans Affairs must start a thorough search for the next director.

“Our veterans deserve the absolute best we have to offer, sadly the VA has fallen tragically short at fulfilling their mission of providing care to our warriors,” Zinke, a former Navy SEAL commander, said in a news release. “The VA must immediately embark on a thorough search for the right person to lead the VA in Montana. It’s time to shake things up at the VA and I think every effort should be made to get the right person in that job.”

Zinke said the department should seek out women leaders to promote. He said women are serving in the military at historic levels and make 80 percent of the health-care decisions in their households.

“Their input and leadership will only bolster the service our veterans were promised,” Zinke said in the release.

U.S. Sen. Steve Daines, R-Mont., also released a statement Wednesday.

“Montana veterans deserve a leader who will ensure their needs are being met and the Montana VA has not lived up to this commitment,” he said. “The Montana VA needs a strong leader who understands the mission and will not fail Montana veterans.”

The announcement comes at a time that local and national officials are trying to fix a struggling VA program that has further limited veterans’ access to care.

More than a year after the federal Veterans Choice program was rushed into existence to serve veterans facing long waits to see a doctor, Montana veterans have said their access to health care is even further out of reach.

In April, Ginnity met during a town hall with Flathead County veterans concerned about their access to health care.

During the April 18 meeting, Ginnity said the VA has been a bureaucracy, but needs to act with a more local focus.

“The VA wanted to put its arms around all the veterans and say, ‘We’ve got it.’ But we can’t. We’ve got to rely on the community partnerships,” he said during the meeting. “For us to continue to do things we do well … it’s building those relationships.”

Reporter Katheryn Houghton may be reached at 758-4436 or by email at khoughton@dailyinterlake.com.