Two men who were apparently part of a demonstration by Jamia Millia Islamia students on Sunday were admitted to the Safdarjung Hospital with "gunshot injury", sources said on Monday.
Delhi Police has, however, denied firing on the protesters during the clash, saying the injuries could be due to the sharp end of tear gas shells.
The father of one of students, Sohaib Khan (23), said his son was not part of the protest but was passing by when he was hit by a "pellet" on toe.
"He underwent surgery last night and was shifted to a ward," his father, Mohammad Arshad, said.
Sohaib is a 4th-year BTech student at Jamia Hamdard, his father said.
Another student, Ajaz (22), who also suffered gunshot injury on the chest apparently at the protest site, was also undergoing treatment at the Centre-run hospital.
According to the police, the force did not carry firearms and did not open fire either.
"The nature of injuries being reported could be due to the sharp end of tear gas shells and we are probing the allegations," a senior police officer said.
The people who were injured in the clash were taken only to Holy Family Hospital and AIIMS trauma centre, he said.