The program has been delayed since last fall because of problems with software reliability and staff training.
But critics of the new health records modernization plan insist the current system can be improved instead of scrapped.
Dr. Terry Adirim has served in the role since late 2021 and will leave on Feb. 25.
The company behind VA's controversial health records project insists the work can still be finished in a way that benefits veterans and taxpayers.
Republican lawmakers want more details on the deaths and assurances that the new VA records system won't cause more harm.
Officials had hoped to start putting the system in new sites early next year, but will now wait at least six more months.
VA leaders expressed major concerns about where the records modernization project currently stands.
Reports of patient harm and cost overruns have threatened to derail the 10-year effort.
The $16 billion project has faced numerous setbacks in recent years.
VA sites in Portland and Seattle were scheduled to start work with the new system later this year.
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