Media reports said the Olympic Council of Asia medical panel had taken up the case after a protest, but it was not immediately clear which team had made the complaint.
Soundarajan took the 800 metres silver ahead of Viktoriya Yalovtseva of Kazakhstan and Zamira Amirova of Uzbekistan.
The panel to decide gender cases includes, among others, a gynaecologist, an endocrinologist, a psychologist and a genetic expert. A range of tests, including a blood test, are carried out.
On Monday, M Karunanidhi, chief minister of Tamil Nadu state, brushed aside the controversy and presented a cheque for $33,500 to Soundarajan for her performance in the Asian Games.
"I do not want to talk about it," the Press Trust of India quoted her as saying when reporters at the presentation ceremony questioned her about the test.
Last year, Soundarajan passed a gender test at the Asian track and field championships in Incheon, South Korea, where she also won silver in the 800 metres.
She also won the gold medal in the 1,500 metres at the South Asian Games in Colombo in August and was declared the best athlete at the Indian national championships in New Delhi in September.