Metropolitan Police said officers discovered the bodies after being called to the home on Vandome Close in Canning Town at about 11.45am on Friday, following “concerns for the welfare of an occupant”.
The bodies of the two women, who have not been identified by police, were found inside a freezer.
The murder investigation is being led by the Metropolitan Police’s Homicide and Major Crime Command and the force said it was working to formally identify the women and trace their next of kin.
This morning police confirmed a man, 50, has been arrested on suspicion of murder.
“They told me that a body had been found, they showed me a photo of a woman but I didn’t know her”
He is in custody at a police station in east London.
This comes as a woman missing for a year from the area was feared to be one of the bodies found in the freezer.
The discovery left residents in the area shaken, with one resident of the block, who did not want to be named, saying: “I’m astonished, it’s a little community.”
“We’re all tight-knit around here, everybody knows everybody,” he added.
Local residents expressed concern for the welfare of a woman from the area who has been missing for 12 months.
A 49-year-old man, who has lived on the street for 18 years and did not want to be named, said he had spoken to police.
“They told me that a body had been found, they showed me a photo of a woman but I didn’t know her,” he said.
“I’ve just heard on the news that it was two bodies. [I’m] just wondering why?”
Scenes of crime officers in protective clothing were at the scene on Monday evening.
Bags of evidence were carried out of the building that contains six flats, while officers guarded the entrance behind police tape.
The glass front door of the block of flats was covered to prevent people seeing inside.
The bodies were found in an area that has seen two fatal stabbings in recent years.
Ahmed Deen-Jah was stabbed to death in a shop on Freemasons Road in April 2017, while 17-year-old Lord Promise Nkenda was attacked by a gang of teenagers and died in nearby Goldwing Close in February 2018.
A 29-year-old local resident, who did not want to be named, said the area suffered from “petty crime” but the discovery of bodies was “unusual”.
He added: “This is not common… it doesn’t put you at ease, you don’t know [under] what circumstances these people were killed.
“When you don’t know, you’re concerned.”