The charity issued an “unreserved apology” to the Government, donors, supporters and the people of Haiti following the revelations.
Announcing her resignation as deputy chief executive, Penny Lawrence said she took full responsibility for what had happened on her watch and was sorry for the “harm and distress” it had caused supporters.
Oxfam has faced intense criticism over its handling of sex allegations, including the use of prostitutes by workers in Haiti in 2011.
The Charity Commission launched its investigation after examining documents provided by Oxfam.
The watchdog said Oxfam may not have “fully and frankly disclosed material details about the allegations at the time in 2011” and it also had concerns about its handling of the incidents since, and the impact that these have both had on public trust and confidence.
The commission’s deputy chief executive David Holdsworth said: “Charities and dedicated, hard-working aid workers undertake vital, lifesaving work in some of the most difficult circumstances across the world.
“However, the issues revealed in recent days are shocking and unacceptable. It is important that we take this urgent step to ensure that these matters can be dealt with fully and robustly.”
Ms Lawrence’s resignation comes after claims the charity was aware of concerns about the conduct of two of the men at the centre of the allegations in Haiti when they worked previously in Chad.
The charity received £31.7m in Government funding in 2016/17, but the support has been put at risk by the scandal.
Four members of Oxfam staff were dismissed and three, including the country director, Roland van Hauwermeiren, resigned before the end of the 2011 investigation.
According to The Times, Oxfam knew about concerns over the conduct of Mr van Hauwermeiren and another man when they worked in Chad before they were given senior roles in Haiti.