The police watchdog has announced it will investigate an incident in which a 13-year-old black child was surrounded by armed police after an officer mistook his water pistol for a real gun.

It comes after the teenager’s mother said she feels “betrayed” by the Metropolitan Police.

The boy suffered soft-tissue injuries after he was rammed off his bike by a police van and handcuffed as he was confronted by marksmen in Hackney, east London, in July.

In a statement read out on her behalf at a press conference on Thursday, the boy’s mother said the incident had been a “deeply traumatic experience” for their entire family, adding that she believed it would not have occurred had her son “been a white 13-year-old boy”.

The Independent Office for Police Conduct (IOPC) originally said the Met Police should investigate the complaint themselves and reiterated the decision upon the force making a second referral containing “new allegations of race discrimination and adultification”.

But the watchdog announced on Friday it had “reconsidered” its decision and launched an independent investigation.

IOPC regional director for London Charmaine Arbouin said: “This was clearly a distressing incident for this boy, his sister and mother and it is right that the complaint is investigated.”

She added: “In the light of the mother’s statement yesterday, and the concerns that have been expressed by the local community in Hackney and more widely, we’ve reconsidered our decision and will now investigate this independently.

“We’ve spoken to the Met and they understand our decision to investigate this independently will enhance transparency.

“We appreciate how upsetting this has been for the family and I hope this will provide assurance to the child’s mother that she has been heard.

“We know that incidents like these also have an impact within policing as well as the wider community, so we will do all we can to conduct this investigation quickly and thoroughly, and will provide updates as it progresses.”

The mother of the boy, who has suffered from nightmares since the incident, said in the statement on Thursday: “I feel let down and betrayed, not only by the police, but also by the IOPC, and by the whole system that is supposed to look after our children, black or white.

“How can I be expected to place my faith in the police to investigate themselves when they have treated my son and me with contempt?”

She added: “I feel broken by it all; distraught because I was not able to protect my child from what happened.”

Campaign group The Alliance for Police Accountability (APA) condemned the treatment of the boy, saying his brightly-coloured water pistol was unmistakably a toy and that the incident demonstrated the “adultification” of black children.

In a written statement, Detective Chief Superintendent James Conway, in charge of policing for Hackney and Tower Hamlets, said he had apologised to the family.

He said: “This incident was understandably extremely distressing for the boy involved as well as the rest of his family.

“We know it may cause public concern and we want to help the public understand why we responded in the way we did.

“This does not in any way detract from our recognition of the trauma caused to the boy, for which I apologised soon afterwards to his family.”