The bodies of the 42-year-old woman and her six-year-old son were found without any apparent indications of suicide or violence, the police said.
A building serviceman had alerted the police to a foul smell coming from the apartment.
The South Korean authorities believe the woman and the boy could possibly have died of starvation based on the statements of the neighbours and the state of poverty that the two lived in, Efe news reported.
Autopsies were being carried out to determine the cause of death.
The police did not find any food in the apartment, and local media reported that the water supply had been cut off due to bills not being paid.
The woman, identified as Han, had escaped to the South from North Korea in 2009, when she married a Chinese-South Korean man, and then moved to China. Later, she returned to South Korea with her son after her divorce.
The Unification Ministry, which assists North Koreans settling in the South, knew about Han's situation and had tried to contact her when she moved to her latest apartment in southwestern Seoul in October, but did not receive any response from her.
A Ministry spokesperson said that the government must do more to help in the integration of the North Korean defectors, especially those who face tougher challenges and are at risk of poverty, according to Yonhap news agency.
More than 30,000 North Koreans have defected the country since the end of the 1950-53 war.
North Korean refugees who arrive in South Korea have to take up a multi-month integration programme and receive temporary government assistance.
However, several NGOs and reports by the government revealed the difficulties this community faces due to factors such as economic and cultural barriers and discrimination as well as alleged scams.
( With inputs from IANS )