PGA Tour commissioner Jay Monahan will step away from day-to-day operations to recuperate from a “medical situation”.
World number two Jon Rahm said many players felt “betrayal from management” after last week’s announcement.
Monahan and the PGA Tour said president Tyler Dennis and chief operating officer Ron Price will lead the organisation in his absence.
“The board fully supports Jay and appreciates everyone respecting his privacy,” the joint statement said.
It added: “We will provide further updates as appropriate.”
The surprise announcement on 6 June that the PGA Tour and DP World Tour would merge with PIF halted pending litigation between the tours, which will move forward as part of the same enterprise.
Tour players were not consulted before the deal was agreed and, at a heated meeting behind closed doors a day later, some players called for new leadership in the organisation.
Monahan, appointed in 2017, previously said those who joined the $2bn (£1.6bn) Saudi-backed LIV circuit when it launched last year would not be welcome back on the PGA Tour.
Ahead of the US Open, Masters champion Rahm, who turned down a reported $200m (£159m) to join LIV, said on Tuesday he was only alerted to the news by text messages.
The deal is being investigated by the US Senate because it believes “PIF’s role as an arm of the Saudi government and the PGA Tour’s sudden and drastic reversal of position concerning LIV Golf raises serious questions”.
Human rights group Amnesty says the announcement is further evidence of Saudi Arabian efforts to draw attention away from the country’s human rights record, a process known as sportswashing.
