Police said the 87-year-old Hwang appears to have died of old age, saying there was no signs of a break-in at his home in Seoul where a security guard was staying together with him.
Police said they will conduct an autopsy to determine the cause of his death.
Hwang defected to South Korea in 1997 after serving in a series of high-level posts in North Korea, including the chairman of the Presidium of the Supreme People's Assembly, Pyongyang's rubber-stamp legislature.
He is also known as the main architect of the North's "juche" or self-reliance ideology, and was said to have tutored North Korean leader Kim Jong-il.
Since his defection, however, Hwang has been a vocal critic of his former communist homeland.