Ex-Save the Children chief executive Justin Forsyth has resigned from Unicef saying he does not want coverage of his past to "damage" the charities.
Mr Forsyth faced three complaints of inappropriate behaviour towards female staff before leaving Save the Children, the BBC reported this week.
He was accused of sending inappropriate texts and commenting on what young female staff were wearing.
He said he "apologised unreservedly" to the three workers at the time.
Mr Forsyth said the reason for his resignation as Unicef's deputy director was not because of what he described as the mistakes he made in his former role at Save the Children.
"They were dealt with through a proper process many years ago," he said in a statement.
"There is no doubt in my mind that some of the coverage around me is not just to (rightly) hold me to account, but also to attempt to do serious damage to our cause and the case for aid."
Meanwhile, Haiti has suspended Oxfam GB operations in the country, as it investigates claims of sexual misconduct by staff in the aftermath of the 2010 earthquake.
Conservative MP Pauline Latham, a member of the House of Commons' International Development committee, welcomed Mr Forsyth's resignation.
"But what I'm more concerned about is the fact he has been able to work for as long as he did," she told the BBC.
"It is shocking. The more I hear about it the more shocked I am. It's terrible for the UK charity sector. It will take a lot of getting over."
Brie O'Keefe, a former employee at Save the Children, said a number of staff were aware of Mr Forsyth's behaviour but were afraid of the consequences of speaking out for the charity.
She told the BBC's Newsnight: "One of the things that kept many of us from speaking out earlier was a desire to protect the organisation that we loved."
She said Mr Forsyth had been brought in to "shake things up" at the charity but it had resulted in "certain toxic leadership behaviours" being tolerated, including temper tantrums, yelling and disrespectful behaviour, and that those who raised concerns would be sidelined from projects.
Ms O'Keefe welcomed Mr Forsyth's apology for the "incidences he created" but added: "He hasn't taken any responsibility for the culture he fostered at Save the Children."
A statement from Unicef said it was grateful to Mr Forsyth for his work over the past two years.
An investigation by BBC Radio 4's PM programme found that the complaints against Mr Forsyth included women receiving a series of inappropriate texts and comments on how they looked, what they were wearing and how he felt about them.
If they did not respond, Mr Forsyth would follow up his messages with an email, asking if they had seen the text.
If they still did not respond, he would ask someone to send them to him for a "quick word".
No formal sanction
Save the Children said it had commissioned "a root and branch review of the organisational culture" at the charity "addressing any behavioural challenges among senior leadership".
The charity said concerns were raised about "inappropriate behaviour and comments" by Mr Forsyth in 2015.
It said two trustees carried out separate investigations into a total of three complaints made by female employees, but there was no finding of misconduct against Mr Forsyth or any formal sanction against him.
"Both reviews resulted in unreserved apologies from the CEO. All the parties agreed to this and the former CEO apologised to the women in question. At that time the matters were closed."
Speaking earlier this week, a spokesman for Unicef said the charity had not been aware of any of the complaints against Mr Forsyth at the time of his recruitment in 2016.
"There have been no such complaints concerning Mr Forsyth at Unicef," he added.
The allegations come after Brendan Cox - the husband of murdered MP Jo Cox - quit two charities he set up in memory of his wife amid allegations of inappropriate behaviour.
The Charity Commission said it had "extensive regulatory engagement" with Save the Children after allegations of misconduct and inappropriate behaviour were made against Mr Cox and Mr Forsyth between 2015 and 2016.