The VA Office of Inspector General has started publishing its findings of investigations launched two years ago into charges that VA medical facilities adjusted patient appointment schedules to meet department standards.

Now the conclusions in at least two of 77 completed investigations have prompted the U.S. Office of Special Counsel and several senators to question the VA watchdog agency's independence, calling for a review of what they say is the IG's "failure to respond to the issues raised."

The OIG released 15 reports on scheduling problems at VA hospitals and clinics in Florida, Iowa and Minnesota on Monday, following complaints from members of Congress and the media that the office was sitting on the investigations, which were completed in 2014.

The reports found procedural aberrations at nine of the 15 facilities investigated, but the VA inspector general noted that in most cases, patient care was unaffected and managers management did not direct employees to manipulate the wait times.

VA officials said Monday that the remainder of the 77 completed investigations will show that the IG found no scheduling irregularities in 25 investigations and found intentional misconduct in 18 cases.

According to VA, it disciplined 29 employees in those cases, "with actions ranging from admonishment to removal."

"This includes three employees who retired or resigned with discipline pending," VA officials noted in a statement.

In two yet-to-be published cases, however, Special Counsel Carolyn Lerner, head of the U.S. Office of Special Counsel, says the VA IG downplayed the scope of its findings of wrongdoing, at Overton Brooks VA Medical Center, Louisiana, and Hines VA Hospital, Illinois. Lerner, investigating whistleblower complaints, sent a letter to President Obama on Thursday objecting to the IG investigations.

Lerner called the investigations "incomplete," adding that they did not adequately investigate whistleblower charges and instead focused on whether separate appointment spreadsheets used by the facilities, that were secondary to the VA's official appointment system, were "secret."

The IG office concluded that the spreadsheets were not secret because employees at the VA hospitals knew about the lists.

"The OIG's decision to investigate this straw man resulted in inadequate reviews that failed to address the whistleblower's legitimate concerns about access to care," Lerner wrote.

A scandal erupted throughout the VA in the spring of 2014 after allegations surfaced that as many as 40 veterans died while waiting for treatment at the VA Phoenix Health Care System.

A 2014 VA inspector general's report found that Phoenix medical center staff manipulated wait lists to meet department standards. The wait time issues and appointment scheduling subsequently were found to be a nationwide problem.

In the wake of the scandal, the VA IG investigated 111 facilities and found problems at 77. The investigation results are either published or pending.

Of the 15 reports released Monday, nine indicate that the facilities either manipulated the scheduling process to make sure that they met a 14-day window for scheduling an appointment, used paper wait lists or spreadsheets to track veterans outside the official appointment system, or failed to enter information correctly.

But in those cases, inspector general staff members concluded that "managers didn't direct" appointment manipulation; that incorrect appointment scheduling was the result of "unintended errors"; paper wait lists were duplicates of the official list; or a separate database was known to management or employees and therefore "not secret."

In no cases did the inspector general find that the procedures harmed patients or led to delays in care.

In her letter to Obama, Lerner said the IG office focused largely on the word "secret" instead of actually reviewing the access-to-care issues raised by VA employees.

Lerner's review of the reports also found evidence that the IG office targeted the whistleblowers who raised concerns about patient wait times.

Lerner said IG staff were disinterested in Brooks VA Medical Center social worker Christopher Shea Wilkes' allegations and that his IG interview was conducted more like a criminal probe into how he obtained the list and whether he shared it with anyone.

Sen. Mark Kirk, R-Ill., released a statement Friday saying Lerner's letter demonstrates that the VA rewards "a culture that attacks whistleblowers instead of protecting vets."

"It's long past time for the VA to conduct a real investigation into whistleblower allegations ... determine how many veterans were harmed and if any died as a result of this scandal, and fire those responsible for covering it up," Kirk said.

VA officials released a statement Monday saying the department has been working since 2014 to improve patient access to care, appointment wait times and employee accountability at VA.

"VA is now well underway on the 'MyVA' transformation, the most significant culture and process change at VA in decades, with the primary goals of putting veterans first and becoming the top customer service organization in government," the statement read.

"We appreciate that, in many instances, the OIG found no intentional wrongdoing; nonetheless these reports demonstrated the need for standardized training on scheduling across [Veterans Health Administration]."

In the statement, VA officials did not refer to Lerner's letter. Instead, they pointed out that the inspector general's position has been vacant for two years.

"There is a nominee currently awaiting confirmation in the Senate to provide guidance and leadership for this organization," officials wrote.

But the nomination of Michael Missal, previously a senior counsel at the U.S. Securities and Exchange Commission, has been awaiting confirmation since last fall and has been held up by various lawmakers.

On Thursday, Sen. Tammy Baldwin, D-Wis., announced she is withholding the nomination over delays in publishing the reports.

"I will hold the nomination of the VA inspector general until I receive a commitment that the inspector general's office will change business as usual and start releasing these reports publicly so we can put solutions in place that solve problems at the VA," Baldwin said.

The office said it would release the remainder of the 77 in the coming weeks.

Patricia Kime covers military and veterans health care and medicine for Military Times.