Chatterjee also issued a ruling that members of the Lok Sabha should keep to their allotted seats and only raise issues from there.
Many MPs, including senior parliamentarians, have already faced Chatterjee's ire over the issue.
As Khanna rose to put a question about basic infrastructure in schools in villages, Chatterjee reminded him that he was not occupying his allotted seat.
"Go back to your seat. I will permit you then," Chatterjee said.
Khanna immediately left his seat in the fourth row and struggled to get to his seat in the next row.
"This is the problem, sir. I am so tall that I cannot bend," he said, referring to a lack of space between the rows of seats.
"So? All MPs should be short?" Chatterjee snapped.
Khanna then pointed out that girl students in villages were removed from schools after they attained puberty due to lack of good toilets and other facilities.
Human Resource Development Minister Arjun Singh said the government would try to introduce "all kinds of measures to maintain students in village schools".