The investigation also found that at least two San Diego VA employees instructed appointment clerks to "zero out" wait times in the scheduling database, presenting an unrealistically positive picture of how long patients were waiting for care.
The VA's inspector general issued the report on Thursday as part of more than 70 investigations it has released nationally over the past few weeks.
The investigations of VA facilities in several states followed a sweeping scandal in 2014 that started over allegations of falsified wait times at the Phoenix VA hospital.
The suicidal San Diego veteran, who was not named in the report, had three or four mental-health care appointments canceled in a row by the VA leading up to his attempted suicide in 2014.
The investigation found that 13 to 14 percent of his appointments were canceled with less than a day's notice in 2013 and, in the following fiscal year, that number rose to between 24 and 27 percent for various clinics.
According to the report, "the veteran stated he used the cancellation of his appointments as an excuse to act out and attempted to harm himself. He said he regrets his actions and that he received help and now has follow-up appointments."
A spokeswoman for the San Diego VA health care system said employees have been held accountable for the scheduling issues, but she declined to identify them.
In total, two staff members retired and two resigned, while two others faced "accountability actions," spokeswoman Cindy Butler said Thursday. One of the people who faced "accountability action" was moved to a job with no scheduling responsibility and the other stayed in the position.
In a statement released Thursday, San Diego VA officials said the inspector general only examined data from early 2014 -- before leaders here made an effort to address the issue.
"VASDHS has aggressively trained and retrained all of our front-line personnel and supervisors to ensure compliance with scheduling procedures," the statement said.
"Regular scheduling audits are conducted and staff are able to clearly articulate scheduling procedures. Where there were allegations and findings were validated, VASDHS took appropriate administrative actions."
Under the 2014 Veterans Choice Act, VA patients facing long wait times can seek care in the private sector, at taxpayer expense. More than 6,000 San Diego veterans have received care through the Choice program since October.
This is the first official sign of trouble at the San Diego VA, which has been touted as a model by local veteran advocates and even VA Secretary Bob McDonald.
The "One VA" committee concept, an idea started in San Diego, brings leaders from the veterans community together with local VA officials on a regular basis to air issues. McDonald has called for the idea to be duplicated nationally.
The inspector general's investigation was prompted by complaints from two San Diego VA employees in May 2014.
They alleged that a national team sent earlier that month to audit the San Diego VA -- in light of the national scandal -- were presented with employees hand-picked and coached to give a glowing picture.
Separately, in June 2014, a VA employee alerted the inspector general's office about the veteran's suicide attempt following canceled appointments.
However, investigators noted that San Diego VA employees first raised concern about manipulated wait times back in 2013, and discrepancies were found in a follow-up inquiry.
But, apparently, that early alarm bell went unheard.
The director of the San Diego VA health care system at the time expressed surprise when faced with the inspector general's conclusions, according to the report released this week.
"He said he was very surprised at our findings as he had spoken to (several employees) regarding the initial allegations and was told there was no altering of desired dates happening in the mental health department," the report said.
Jeff Gering was the San Diego director from May 2012 until late December, when he left for a job at another San Diego health care system.
The investigation found that an unnamed San Diego VA medical administrative officer put pressure on "medical support assistants" -- the people who schedule appointments -- to "zero out" the number of days that a veteran was waiting for an appointment.
Also, a mental health program analyst played a role.
In emails sent in April 2014, the analyst advised schedulers to call patients with wait times more than 14 days past their desired appointment dates and offer them earlier visits.
If the veteran declined the earlier appointment date, the scheduler was told to change the veteran's desired date to the original appointment date -- making it appear there was no wait time.
"The employee stated that, at the time, she thought that she was correct, but had now come to understand it is not the proper way to capture desired dates," the report said.
The report notes that the VA directive on wait time policy is from 2010.
In an odd twist, the VA this week also released results of an investigation that did not substantiate an allegation of pressure to "fudge" wait times at the San Diego VA.