WASHINGTON - A top federal investigator has identified "a troubling pattern of deficient patient care" at Veterans Affairs facilities around the country that she says was pointed out by whistleblowers but downplayed by the department.

The problems went far beyond the extraordinarily long wait time for some appointments - and the attempts to cover them up - that has put the department under intense scrutiny.

In a letter Monday to President Barack Obama, Carolyn Lerner of the U.S. Office of Special Counsel cited canceled appointments with no follow up, drinking water contaminated with the bacteria that causes Legionnaires' disease and improper handling of surgical equipment and supplies.

Acting VA Secretary Sloan Gibson said he had launched a departmental review due to be completed within 14 days. "I am deeply disappointed not only in the substantiation of allegations raised by whistleblowers, but also in the failures within VA to take whistleblower complaints seriously," he said in a statement.

The letter did not specifically site any complaints stemming from the Charleston VA Medical Center, but at least one whistleblower has raised concerns here before.

In 2012, a nurse practitioner at the Charleston VA Medical Center alleged that three other nurse practitioners working within the mental health service line were unqualified because they were not certified to work with psychiatric-mental health patients. The whistleblower said her peers were prescribing psychotropic medications to veterans with a variety of diagnoses, including post-traumatic stress disorder, schizophrenia, bipolar disorder and major depression.

While the VA eventually acknowledged that two of the three nurse practitioners cited in the complaint were violating state licensure laws and VA rules, investigators determined that the breach did not compromise patient care. The case was officially closed on Feb. 11.

Lerner said the VA consistently acknowledges problems but says the quality of patient care is not affected, which she referred to as "the VA's typical harmless error approach."

"This approach has prevented the VA from acknowledging the severity of systemic problems and from taking the necessary steps to provide quality care to veterans," Lerner wrote to Obama. "As a result, veterans' health and safety has been unnecessarily put at risk."

Complaints about a lack of access to VA health care have prompted a national outcry that led to VA Secretary Eric Shinseki's resignation. The most startling allegations have arisen out of the VA's medical center in Phoenix, where a VA inspector general's investigation found that about 1,700 veterans in need of care were "at risk of being lost or forgotten" after being kept off an official, electronic waiting list.

Lerner says the office is reviewing more than 50 complaints alleging threats to patient health and safety and has referred 29 of them to the VA for investigation.

On Monday, Charleston VA Medical Center spokeswoman Tonya Lobbestael said she was not aware that the federal government intended to review the Charleston case again.

"We have not been notified of anything of the sort," she said. "As far as we know, nothing on our end, which is good news."

Lerner's office is an independent investigative and prosecutorial agency that protects federal workers from prohibited personnel practices, especially reprisal for whistleblowing.

Lerner said two cases highlight her concerns. In Fort Collins, Colorado, the VA's Office of Medical Inspector confirmed multiple violations of policy concerning appointment scheduling and cancellations that masked true wait times. Nearly 3,000 veterans were unable to reschedule cancelled appointments, and one nurse practitioner alone had 975 patients unable to reschedule appointments. However, the same office did not substantiate that the failure to properly train staff resulted in danger to public health and safety.

Lerner said the VA's conclusion "is not only unsupportable on its own, but is also inconsistent with reports by other VA components examining similar patient-care issues."

In a second case, a VA psychiatrist disclosed concerns about patient neglect in a long-term mental health care facility in Brockton, Massachusetts. One veteran who was a resident of the facility between 2005 and 2013 had only one psychiatric note written in his chart. Another was admitted to the facility in 2003, yet his first comprehensive psychiatric evaluation did not occur until 2011.

Despite the findings, the VA said there was no impact on patient care. A follow-up was requested, and the VA again said it did not feel that the patient's rights were violated.

"Such statements are a serious disservice to the veterans who received inadequate patient care for years after being admitted to VA facilities," Lerner wrote. "Unfortunately, these are not isolated cases."

She cited other cases in Buffalo, New York; Little Rock, Arkansas; Harlingen, Texas; Jackson, Mississippi, and San Juan to bolster her position that the VA is downplaying the impact of deficient care.

Rep. Jeff Miller, the Republican chairman of the House Committee on Veterans' Affairs, said Obama needs to reiterate to each VA employee the need to solve problems rather than downplay them.

"It's impossible to solve problems by whitewashing them or denying they exist," Miller said.

Sen. Bernie Sanders, the chairman of the Senate Committee on Veterans' Affairs, said the concerns of whistleblowers must be addressed promptly and effectively.

The VA said Gibson had reiterated to staff earlier this month that whistleblowers must be protected.

Both the House and Senate have passed legislation that would require the VA to pay private providers to treat qualifying veterans who can't get prompt appointments. Each chamber has appointed a committee to iron out differences between the two bills, with the lawmakers meeting Tuesday.

Both bills would make it easier to fire or demote senior agency officials, and both would end bonuses to regional VA officials and other administrators based on meeting patient scheduling goals - a practice investigators say led some officials to create phony waiting lists to "game" the system.

Charleston VA Medical Center Scott Isaacks told The Post and Courier in early June that no secret waiting lists exist at the local hospital.

Post and Courier reporter Lauren Sausser contributed to this report.