In her petition, the 37-year-old officer has claimed that the IAF's decision to deny her a permanent commission was "biased, discriminatory, arbitrary and unreasonable."
"IAF says Pooja Thakur was offered a permanent commission in 2012. She declined it then, and it can be offered only once. No new offer can be given," her lawyer, retired Major Sudhanshu Pandey, told media.
Thakur, who joined the IAF in 2000, became the first lady officer to lead an Inter-Service Guard of Honor, when President Obama visited India as a chief guest for the Republic Day parade in January 2015.
Obama had later said at the event that the sight of "incredible" Indian women in the armed forces was one of his "favorite things" in the country.
The tribunal admitted the matter and has sought the IAF's response within four weeks, Thakur's lawyer added.