The 10-12kg (22lbs - 26lbs) chunk of ice fell on Fazilpur Badli village with a "big thud", startling residents on Saturday.
Senior Gurgaon official Vivek Kalia told the BBC some villagers thought it was an "extra-terrestrial" object.
Plane toilets store human waste in special tanks.
These are normally disposed of once the plane has landed. But international aviation authorities acknowledge that lavatory leaks can occur in the air.
Mr Kalia told the BBC that a sample of the projectile had been sent for chemical analysis, but "we suspect strongly" that it is frozen airline excrement.
"It was a very heavy icy ball of ice which dropped from the skies early on Saturday morning. There was big thud and people of the village came running out of their homes to find out what had happened," he said.
"Some villagers thought it was an extra-terrestrial object. Others thought it was some celestial rock and I've heard that they took samples home," he said.