The GMB trade union has launched an investigation into allegations involving their departing General Secretary Tim Roache.
A powerful union committee has formally accepted Mr Roache's resignation.
His decision to go was announced on Tuesday night and took many by surprise - not least some of the union's most senior officials.
He had been re-elected to his post last year, having first being elected to the union's most senior position in 2015.
In statement on Wednesday night, the union said Mr Roache had been diagnosed some years ago with ME, also known as chronic fatigue syndrome (CFS).
The union said medical professionals had now advised him to refrain from work and he did not feel mentally or physically able to continue to lead his organisation.
But the decision seemed to have coincided with what is thought to be a campaign by a group of people calling themselves "concerned GMB staff and members," who were calling for him to be suspended from office.
The BBC has seen a letter sent to the union's President Barbara Plant.
It makes several unsubstantiated allegations about Mr Roache's conduct, including an allegation of impropriety.
Mr Roache has not responded to calls from the BBC but in a statement, the union said: "The GMB received an anonymous letter last Wednesday in which a number of allegations were made about Tim's conduct.
"An investigation has been launched. It is not appropriate to comment further."
His departure comes soon after a change of Labour leadership and the leak, earlier this month, of an internal party document which denounced "factionalism".
The document contained controversial private WhatsApp messages between staff.
These included messages seen as damaging to a former staff member who was being tipped in Labour circles as a future Labour general secretary.
Tim Roache and some of his senior GMB officials were seen as unhelpful by those close to the previous Labour leadership.
He backed a "final say" referendum on Brexit, and the union supported Owen Smith's unsuccessful challenge to Jeremy Corbyn's leadership in 2016. It also supported Lisa Nandy's party leadership bid this year.
GMB members on Labour's ruling National Executive Committee were supportive of the new party leadership at a recent meeting.
The question now is whether new leadership at the GMB will remain supportive of the new leadership of the Labour Party.
For the time being, the GMB regional secretary for Wales and South West, John Phillips, will become acting general secretary of GMB and the union has said it is "considering a process and timetable" to elect a permanent replacement as soon as practically possible.