US Veterans Affairs Secretary Eric Shinseki has resigned after taking public responsibility for widespread failures in health care for US war veterans.

President Barack Obama accepted the resignation on Friday after a morning meeting with the retired four-star general just two days after a scathing internal report found broad and deep-seated problems in the sprawling health care system, which is struggling to keep up with the number of vets returning from Iraq and Afghanistan.

The report prompted loud calls for Shinseki to resign from congressional Republicans and Democrats.

Shinseki was accused of allowing hospitals to cover up massive delays in appointments.

Shinseki took responsibility for the leadership and integrity problems that were first found at a facility in Phoenix, Arizona, but are now part of a larger investigation involving others across the country.

The initial report alleged that up to 40 war veterans died while waiting for healthcare in Phoenix.

"We now know that VA has a systemic, totally unacceptable lack of integrity within some of our veterans’ health facilities," he said. "That breach of integrity is irresponsible; it is indefensible and unacceptable to me."

The embattled secretary said he had been led to believe the problems were limited and isolated but that he had been too trusting.

"Given the facts I now know, I apologise as the senior leader of Veterans Affairs," he said, adding that the leadership and integrity woes at the VA can be fixed.

He announced several changes, including the removal of senior leaders at the Phoenix facility. He also called on Congress to pass legislation addressing the issue.

The report confirmed earlier allegations of excessive waiting times for care in Phoenix, with an average 115-day wait for a first appointment for those on the waiting list _ nearly five times as long as the 24-day average the hospital had reported.

The ageing network of hospitals and clinics - the VA opened its first new medical center in 17 years in 2012 - is one of the world's largest integrated health care systems.

The VA estimates the US has more than 21 million veterans, men and women who fought in World War II through the wars in Iraq and Afghanistan. The largest group is Vietnam War veterans, who need more care as they age.

Source: Agencies