Her sample was taken late Tuesday evening by local health authorities from her parental residence near Hamirpur town in the hill state after the first one failed.
Kangana was now scheduled to take flight from Chandigarh at 12.15 p.m. on Wednesday to Mumbai.
However, the tests of her sister and assistant were negative.
In a tweet en route to Chandigarh via road, she said, “I have lived the courage, valour and sacrifice of Rani Laxmibai through my films. The sad thing is that I am being prevented from coming to my own Maharashtra. I will continue to raise my voice against wrong, Jai Maharashtra, Jai Shivaji.”
The family of Kangana was settled at Bhambla village near Hamirpur town, some 200 km from the state capital Shimla.