The inquiry is being led by the complex case team of the Sexual Offences, Exploitation and Child Abuse Command.
Kids Company said it was not aware of the nature of any allegations and its priority was the safety of its clients.
Police want anyone with information or concerns to contact them or the NSPCC.
The police investigating team can be contacted on 0208 217 6538, while the NSPCC helpline number is 0808 800 5000.
Kids Company is run by Camila Batmanghelidjh.
The charity provides practical, emotional and educational support to some of the most deprived and vulnerable inner-city children.
In a statement Kids Company said its "first priority is the safety and security of all the children, young people and adults we support and protect".
It added: "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 misconduct between Kids Company employees and clients are immediately reported to the police if required."
Earlier this month the charity faced questions about the way it was run and whether government funding would continue.
An investigation into a number of allegations of crime involving the children's charity Kids Company has been launched by the Metropolitan Police, the BBC has learned.