Liverpool Clinical Commissioning Group's (CCG) chief officer Katherine Sheerin and chief finance officer Tom Jackson have both left their posts.
In June, the CCG's deputy chairwoman Prof Maureen Williams quit after a committee she chaired was criticised for making decisions on pay increases.
The CCG has made no further comment.
Ms Sheerin, who has worked for the CCG for five years, said after 25 years in Liverpool, she had "decided it is the right time to move on", while Mr Jackson said that following his colleague's resignation, "I too have decided to stand down".
The government ordered a review into the CCG in March after Rosie Cooper, the Labour MP for West Lancashire, raised concerns about pay increases for governing body members between 2013-14 and 2014-15.
Most of the pay rises related to the 2014-15 financial year, when chairman Dr Nadim Fazlani's salary rose from approximately Â£105,000 to Â£155,000.
The review said the remuneration committee, of which Prof Williams was chairwoman, had "acted outside its terms of reference" by making decisions on pay increases, rather than making recommendations.
It also highlighted conflicts of interest, particularly in the CCG's first year of operation in 2013-14, which "were not managed robustly with a lack of independent advice and scrutiny of decisions".
Two NHS officials whose pay rises were reviewed as part of a government investigation of their clinical commissioning group have resigned.