Police said officers discovered the bodies after being called to the home in Vandome Close, Canning Town, at about 11.45am on Friday.
A murder investigation has been launched and the Metropolitan Police said it was working to formally identify the women.
One is believed to be Mary Jane Mustafa, a 38-year-old mum of two who vanished mysteriously last May.
Back in January, Mary Jane’s cousin Ayse Hussain had called for help in finding her.
“Ali called him back later and said ‘There’s something you should know – I’ve killed some women’”
She said: “She’s missed her own birthday, her daughter’s birthday and now Christmas.
“I’ve been looking after her kids now and then, and I took her daughter Christmas shopping to keep her distracted.
“We just say mum has gone to sort herself out and say she’ll be back soon.
“Her daughter has just started secondary school and her son is 19.”
Last night on Facebook, her sister Zeynep Mustafa Sukan wrote: “When are you coming home, sis? I miss you like you wouldn’t believe!”
No arrests have yet been made and no details of any suspect have been formally released.
A resident alleged The Sun that a man, known as Ali to neighbours, was friends with Mary Jane and he had made a horrific admission.
One resident said: “My mate saw Ali on Thursday and he looked anxious and scruffy.
“When the police turned up on Friday, Ali had disappeared.
“My mate phoned Ali and said there were loads of police at his flat – loads of them. Then the phone went dead.
“Ali called him back later and said ‘There’s something you should know – I’ve killed some women’.
“Later on my mate saw the police take away a big chest freezer from Ali’s place.”
He added: “Ali used to hang around with Mary Jane. She went missing a year ago and they’ve been searching for her ever since.”
Scenes of crime officers in protective clothing were at the scene last evening.
Bags of evidence were being carried out of the building that contains six flats, while officers guarded the entrance behind police tape.
Detective Chief Superintendent Richard Tucker said: “The launch of any murder investigation is naturally of concern to the local community and we have borough officers in the area supporting colleagues from the Homicide and Major Crime Command as they investigate the full circumstances.
“A crime scene is in place and we would encourage anyone with information about what may have happened at this premises to contact police on 101, quoting CAD 4303/26APR.”