It has not given a reason for the withdrawal, the SEA Games 31 Organizing Committee said Friday.
It said that the Indonesian Olympic Committee has affirmed in a written statement that only men will participate in the football and futsal events.
The schedule for the women's events in these two sports will have to be adjusted and publicized in the near future, the organizing committee said.
As per the draw, Indonesian women footballers were placed in Group A with host nation Vietnam, the Philippines and Cambodia. Group B consisted of Thailand, Myanmar, Laos and Singapore. The top two teams from each group would advance to the semifinals.
Without Indonesia, remaining women's futsal teams are Vietnam, Thailand, Malaysia and Myanmar.
The SEA Games 31 will take place May 12-23 in Hanoi and 11 northern provinces – Bac Giang, Bac Ninh, Ha Nam, Hai Duong, Hai Phong, Hoa Binh, Nam Dinh, Ninh Binh, Phu Tho, Quang Ninh and Vinh Phuc.
The contestants will compete in 40 sports with 520 categories.