Malik, who hails from Haryana, was the first Indian woman athlete to win a medal at the Paralympics in Rio.
She won a silver medal in the women's shot put event with a throw of 4.61m at the paralympics.
Modi, who was sitting on a dais along with Haryana Governor Kaptan Singh Solanki and Chief Minister Manohar Lal Khattar, came down and walked a few steps to honour Malik, who was on a wheelchair.
Modi handed over the cheque to Malik in the presence of Khattar and Haryana's Sports and Youth Affairs Minister Anil Vij.
Complimenting the state for substantial improvement in sex ratio, Modi said he is grateful to females and elders of Haryana for responding to his appeal of 'beti bachao, beti padhao'.