A Cape Town family is reeling after discovering the body of their 5-year-old son in the aftermath of a fire that engulfed their home on Wednesday, police say.

Cape Town community radio station Radio 786 reported that the home belonged to Gaierronessa Meyer in Amandel Street, in Bonteheuwel.

According to Western Cape police, the family said the 5-year-old had gone missing, but when the fire was doused and crime scene experts started combing the scene, they made the shocking discovery.

Police spokesperson Captain FC van Wyk said the blaze started in the house, but fire and rescue services officials were able to stabilise it.

"This morning (Thursday), the victims were busy cleaning the remains and they discovered the shocking burnt body of their minor who was missing since last night," said Van Wyk.

An inquest docket has been opened for investigation, Van Wyk said. 

Van Wyk added that crime scene experts were looking for crucial evidence that would assist.