Authorities have identified her as Siti Aisyah, 25, originally from Serang in Banten, a province that neighbours the Indonesian capital, Jakarta. She was arrested by Malaysian police early on Thursday.
Indonesian Immigration Office spokesperson Agung Sampurno said that officials from the Indonesian Embassy in Kuala Lumpur met with the woman in Selangor state, where she has been imprisoned, and ensured she was safe.
"They were allowed to see her but cannot make any questions," said Sampurno. "However, the team can confirm that Aisyah is Indonesian."
He said a passport ID page published by Indonesian media is "the same as the passport held by her."
Lalu Muhammad Iqbal, director of Indonesian Citizen Protection at the Foreign Ministry, said Indonesia would ensure Aisyah's rights are protected and that she has legal assistance.
Malaysian police have now arrested two women and one man in the death of Kim Jong Nam, who was reportedly poisoned on Monday by a pair of female assassins as he waited for a flight at the Kuala Lumpur airport.
Malaysian police said the first woman they arrested had Vietnamese travel documents. Vietnamese Foreign Ministry's Deputy Spokesperson Nguyen Phuong Tra said in a statement that Vietnamese authorities were closely coordinating with Malaysia on the case.
Kumparan, an Indonesian news portal, said Aisyah lived in the Tambora neighbourhood in western Jakarta for about 10 years before moving to Malaysia in 2013 along with her husband and children. It cited interviews with former neighbours and said she had returned to Indonesia in 2014 to arrange a divorce.
Sampurno said immigration data showed that Aisyah had visited Indonesia earlier this year and returned by ferry to Johor, Malaysia, from the nearby Indonesian island of Batam on February 2.
Several million Indonesians work in Malaysia as maids and construction and plantation workers.
Investigators in Malaysia are trying to shed light on the death of Kim, which has set off waves of speculation over whether North Korea dispatched a hit squad to kill him.