"It is a petty matter. It was an accident. It's very unfortunate. It is not police assault," she said on a trip to Bangalore.
Mr Gupta was a member of the Students Federation of India (SFI), which says that he was beaten repeatedly on the head by the police when it arrested a group of activists protesting against Ms Banerjee's decision to postpone college union elections. The SFI is the youth wing of the CPI(M).
Ms Banerjee has backed the police, which says he hit his head on a lamp-post when he fell out of a bus that was meant to move the arrested students to prison.
Mr Gupta, 22, was cremated on Wednesday night with thousands lining the streets to pay tribute to him.
An autopsy report shows Mr Gupta had a broken jaw and fractures on his head as well as injury marks all over his body, and that all the injuries were sustained before his death.
The Kolkata Police has come out strongly contradicting the post mortem report. The police said that the head injuries suffered by Mr Gupta indicated that he had run into a blunt, stationary object.
"Death due to head injuries... And no injuries due to lathis or rods... He hit head on lamp post," said Javed Shamim, Joint Commissioner of Police, Law & Order, Kolkata.
The State Human Rights Commission will investigate the death, and has asked the police to submit a report within a week.
"My son's death was not an accident....I want justice," said Mr Gupta's father, Pranab Gupta, to NDTV today.
His daughter created a controversy last night when she said on a television channel, "The CPM brainwashed my brother. The leaders used him for the party's interest."
Today, she clarified that her remarks had been made under emotional stress.
"Our appeal to the media is please don't jump to a conclusion because the way the incident is being projected is not right. We have launched a thorough investigation and the forensic team has visited the spot," Joint Commissioner of Police (Hqs) Javed Shamim said.