The investigation is being led by officers from Scotland Yard’s Complex Case Team of the Sexual Offences, Exploitation and Child Abuse Command.
Police have declined to give any details of the multiple allegations.
Reports suggest that the investigation into Kids Company is believed to have been triggered by a testimony from a former employee given to a BBC Newsnight and BuzzFeed News investigation.
Kids Company said it understood the serious allegations to be historical.
In a statement the charity said, ‘Kids Company is co-operating fully with the Police to assist the investigation into what it understands to be historical but serious allegations, which have no further substantive information to date.
‘Kids Company’s first priority is the safety and security of all the children, young people and adults we support and protect. The organisation operates robust policies and procedures that ensure all Kids Company’s clients are protected and that staff work safely with clients at all times. Kids Company’s policies and procedures are externally reviewed regularly by an expert consultant and are governed by a risk sub-committee comprised of senior clinicians and representatives from the board of trustees.
‘All allegations of criminal behaviour regarding Kids Company employees and clients are immediately reported to the police.’
Earlier in the month, the charity’s founder Camilla Batmanghlidjh announced she is to step down as chief executive following a row with the Government.
Kids Company, which relies heavily on public funding, was allegedly told by Government officials it would not receive £3m in funding unless she was replaced.
The Government reportedly has concerns over mismanagement of funds at the charity.
Ms Batmanghelidjh denied Kids Company has been mismanaged, telling BBC Radio 4’s Today programme that the claims are a ‘red herring’ to avoid the ‘real issues’.
She also said she had always planned to stand down in her 20th year in 2016.
The charity confirmed that Ms Batmanghelidjh will assume an advocacy and clinical role after a new chief executive is appointed.