The program has been delayed since last fall because of problems with software reliability and staff training.
VA Deputy Secretary Donald Remy to depart, after serving in the post since July 2021.
Dr. Terry Adirim has served in the role since late 2021 and will leave on Feb. 25.
New legislation would block further deployments of the controversial system until VA leaders can promise permanent improvements.
Rollouts of the controversial system are expected to resume next summer.
Republican lawmakers want more details on the deaths and assurances that the new VA records system won't cause more harm.
A system issue forced the health records offline for a day last week, disrupting medical operations at a Washington state site.
VA leaders say they are committed to the Cerner-based technology but still unsure of the implementation timeline.
GAO officials said work should halt until fixes are in place, but VA officials said they can make corrections without delaying any deployment plans.
Officials recently pushed a planned initial deployment of the electronic records system back from this month to July.
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