Stuart Hazell, aged 37, is accused of killing Tia Sharp, who went missing in New Addington, south London, more than a week ago.
Mr Hazell is the partner of Tia’s grandmother, Christine Sharp.
Ms Sharp has been released on bail following her arrest on suspicion of murder, Scotland Yard said.
Officers have also freed Ms Sharp’s next-door neighbour on bail pending further inquiries.
Paul Meehan, aged 39, was detained by detectives on suspicion of assisting an offender.
Police arrested the three suspects on Friday after investigators discovered a body inside the house Mr Hazell shares with Ms Sharp, aged 46, in The Lindens, New Addington, near Croydon. The property was the last place where Tia was seen alive. The body has not yet been formally identified but is believed to be Tia’s.
Mr Hazell was charged during the early hours of yesterday morning after being quizzed by detectives.
A massive manhunt was launched for Tia after she was reported missing by her family nine days ago.
Despite visiting Ms Sharp’s terraced property four times, investigators only found the body on Friday.
An autopsy on the body is expected to recommence today after it was paused last night.
Neil Basu, Metropolitan Police south-east London area commander, said that “human error” was to blame for not locating the body sooner and apologised to Tia’s mother Natalie.
Mr Basu explained the first examination of the property on receiving the report last Friday was not a full search. He said mistakes were made on the second search two days later, which took two hours.
“All parts of the premises were searched including the location where a body was discovered, five days later.”
Meanwhile, Tia’s mother was overcome with emotion as she visited the site where scores of people have left tributes to her daughter.
Natalie Sharp wept as she surveyed the sea of flowers and cards on the pavement close to the property, hours after the grandmother’s partner Stuart Hazell, 37, was charged with murder.
A note believed to have been left by Ms Sharp read: “Our baby girl, we love you very much and always will.
“Sorry baby that this has happened, I wish I was there to protect you.
“We know you are safe now and you are at home with us everywhere we go. Love you, mum, dad, Jack and Harry. XXX”.