The London School of Economics (LSE) and its students' union have demanded the BBC withdraw Monday's Panorama programme about North Korea.
The LSE said Panorama reporter John Sweeney posed as one of its professors on a study trip in order to film undercover in the country.
The union's Alex Peters-Day said the BBC used students "as a human shield".
Sweeney said the students were told a journalist was with them but that the LSE was not as it was not an LSE trip.
Speaking to BBC Radio 4's Broadcasting House programme, Sweeney said: "For the LSE to put words into the mouths of those LSE students... is extraordinary. For them to say kill this programme - that feels entirely wrong.
"What the LSE is saying we dispute. I can't talk for those students - they are grown-up, they are brave and good people.
"All of those students could have dobbed me in. They didn't, the majority of these students support this programme."
Sweeney spent eight days undercover inside North Korea for the programme. He travelled with his wife and a cameraman.
Sweeney described North Korea as a "Nazi state" that practised the "most extreme form of censorship".
He added: "It's more like Hitler's Germany than any other state in this world right now. It's extraordinarily scary, dark and evil."
But the LSE students' union general secretary, Ms Peters-Day - who was not on the trip - told the BBC News channel: "One of the students made it absolutely clear that she was not made aware of what happened.
"For us, this is a matter of student welfare - students were lied to, they weren't able to give their consent."
She said all LSE's future research was "now at risk".
"I think the trip was organised by the BBC as potentially a ruse for them to get into North Korea and that's disgraceful.
"They've used students essentially as a human shield in this situation."
In an email sent to LSE students and staff, the university said: "It is LSE's view that the students were not given enough information to enable informed consent, yet were given enough to put them in serious danger if the subterfuge had been uncovered prior to their departure from North Korea.
"While this particular trip was run in the name of a student society, the nature of LSE's teaching and research means that aspects of North Korea are legitimate objects of study in several of our academic disciplines.
"The BBC's actions may do serious damage to LSE's reputation for academic integrity and may have seriously compromised the future ability of LSE students and staff to undertake legitimate study of North Korea, and very possibly of other countries where suspicion of independent academic work runs high."
It said the LSE was "fully supportive of the principle of investigative journalism in the public interest" but could not condone the use of its name, or the use of its students, "as cover for such activities".
It also said two other people working for the BBC also went on the trip. "At no point prior to the trip was it made clear to the students that a BBC team of three had planned to use the trip as cover for a major documentary to be shown on Panorama," it added.
The LSE said BBC director general Lord Hall refused its request to withdraw the programme and "issue a full apology to LSE for the actions of BBC staff in using the school and its good reputation as a means of deception".
A student who went on the trip, wishing to remain anonymous, told the Beaver that "we were not made aware of the presence of several BBC journalists at the time of the flight to Pyongyang. We were led to believe that John Sweeney was a history professor, although it was later implied that he was not a professor at the LSE."
Also on Twitter, Craig Calhoun, the director of the LSE, said the "BBC story put LSE students at danger but seems to have found no new information and only shown what North Korea wants tourists to see".
A BBC spokesman said: "We recognised that because it could increase the risks of the trip, the students should be told in advance that a journalist intended to travel with them, in order to enable the students to make their decision about whether they wanted to proceed.
"They were given this information, and were reminded of it again, in time to have been able to change their plans if they wanted to. The students were all explicitly warned about the potential risks of travelling to North Korea with the journalist as part of their group.
"This included a warning about the risk of arrest and detention and that they might not be allowed to return to North Korea in the future."
Panorama: North Korea Undercover can be seen on BBC One at 20:30 BST on Monday.