An article on the BBC website on Friday claimed that Adrian Bell, who had been chief excutive for eight years, had stepped down in June. The BBC said a leaked report showed that he had left after claiming the charity's chair, Dr Helen Bowcock, acted to "intimidate, humiliate and belittle" staff.
Bowcock said trustees had acted swiftly after hearing of the allegations.
The BBC said the leaked independent report examined the allegations and called for a further review of workplace culture.
The report’s author said they did not find there was "intentional bullying or intimidation of staff" at the charity but they were "struck by the level of fear and apprehension in staff, and their feelings of powerlessness", according to the BBC.
A spokeswoman for the commission said: "The commission is aware of allegations relating to bullying and harassment at the Kent, Surrey and Sussex Air Ambulance Trust.
"Anyone involved in a charity has the right to feel protected and free from harm, so issues around safeguarding are of serious concern to the commission."
She said the commission was aware that an independent review was under way at the charity.
"We are currently analysing information provided and will be engaging with the trustees to assess their handling of the concerns and determine our next regulatory steps," she said.
Bell takes up a new role as chief executive of the Royal Navy and Royal Marines Charity in September.
In a statement to Third Sector, Bowcock said: "The trustees acted swiftly on receipt of a concern outlined by Adrian Bell in late April 2018.
"We retained an independent assessor, informed the Charity Commission and, on receipt of the assessor’s report, accepted its findings and approved its recommendations for immediate action.
"We would like to thank Adrian for the good work that he has done for the charity over the last eight years and wish him all the best as he takes up this role.
"Meanwhile, the board of trustees will support the KSSAAT team in achieving world-class research, pre-hospital care and impressive life-saving clinical outcomes for the 4.7 million people across 3,600 square miles in Kent, Surrey and Sussex."
A Care Quality Commission report, published in June after an inspection in March, praised the "genuine positive culture and commitment to developing staff" at the charity’s headquarters and said staff "felt respected and valued".
Third Sector was unable to contact Bell for comment.