The Fire and Rescue Department told reporters that their station in Tenom received a distress call at 8.08am and dispatched two fire engines a minute later.
The fire trucks arrived at the scene, about 30km away, 20 minutes later and doused the blaze at 9am.
The 20-year-old woman and boy, aged three, were found in the living room of their People’s Housing Project (PPR) unit, 90% of which was destroyed.
Sixteen firefighters were involved in putting out the fire with investigations into the cause of the fire already under way.