The deceased were Manju, 40, and her children Tanu, 2, and Daksh, 4, police said.
The Delhi BJP accused the Aam Aadmi Party-led government of "criminal negligence", saying the accident was caused due to water logging in the area for a long time as the Delhi government had laid sewer lines there.
The AAP has denied the charges, saying that the BJP-led MCD was in charge of drainage and water-logging.
The fire brigade received a call of building collapse from Mohan Colony at 2.46 a.m., a fire officials told IANS.
"A portion of the roof of the first floor building in which the victims were staying collapsed, resulting in the three deaths," Deputy Commissioner of Police (West) Pushpendra Kumar told IANS.
The officer said no construction was going on in the building.
"The building was old and probably in bad condition, that's why it fell," the officer said.
The woman's husband sustained minor injuries and was shifted to hospital, police added.
According to area residents, the Delhi Jal Board has been laying drain pipes for the past two years but the work has not been completed yet.
"During rains, water accumulating in the pipeline enters the houses," area resident Mukesh Sharma told IANS.
"Sewerage work of the DJB in the area coule have led to the incident," he added.
Delhi Bharatiya Janata Party chief Satish Upadhyay, who met the family of the deceased, attacking the AAP government, said: "It's criminal negligence on part of Water Minister Kapil Mishra, AAP MLA Naresh Balyan, officials of the DJB (Delhi Jal Board) and the DSIIDC (Delhi State Industrial and Infrastructure Development Corporation)."
Upadhyay said Mishra and Balyan had full knowledge about waterlogging in about 20 houses in the area due to "negligence" in the work of laying sewer lines.
"They did not take any concrete steps to solve this problem though the locals had brought this case to the knowledge of Chief Minister Arvind Kejriwal and Deputy Chief Minister Manish Sisodia several times," he said.
Balyan, the AAP legislator from Uttam Nagar, denied the BJP's allegations terming them as baseless. "All the allegations of the BJP are baseless," Balyan told IANS.
"No politics should be done on this issue," he said, adding that "drainage and waterlogging issues lie with the MCD (municipal corporations of Delhi)".
DJB officials could not be contacted despite repeated attempts.