The flatmates were told of what happened and the matter was resolved in a way the university was confident was to their advantage.
The bongs, which the flatmates acknowledged had been used for consuming illegal drugs were destroyed.
"The Proctor is often called on to make judgments as to how to manage difficult situations and in doing that he gives careful thought to the interests of students
involved."
Student magazine Critic Te Arohi reported that about three weeks ago, proctor was visiting flats on Castle St and Leith St North to deliver letters about initiations.
"The entire flat was away, apart from one person who was asleep upstairs.
"The flatmates said the proctor let himself in through the unlocked back door, where he found several water pipes sitting out on a table and took them," the magazine said.
"Because they weren't home, the flatmates didn't know what had happened to the pipes and assumed they had been robbed. They estimated the pipes were worth $400."
The proctor returned the next day, and told them that he had gone into their flat and confiscated the pipes.
According to the flatmates, he told them that as long as they cleaned up the flat, he would let them off with a warning and wouldn't take it to the police, Critic reported.
OUSA recreation officer Josh Smythe told the Otago Daily Times he had been contacted by the flat who complained to the Critic and students from three other flats, saying the proctor had taken bongs after entering the flats via the back door to deliver letters warning about the dangers of initiations.
In the other instances flat members were home at the time he visited, but Smythe said it was "pretty outrageous" Scott felt he could simply wander in, leaving the students concerned feeling very intimidated.
On one occasion the "bong" was simply a Powerade bottle on the flat's living room table.
He had arranged to meet Scott about the situation today, but Scott had since cancelled the meeting.
A protest was being held at 1pm on Friday.
He would be meeting with Scott today about the situation and said some students at the university had been considering having a protest.
OUSA president Caitlin Barlow-Groome earlier told RNZ entering flats without permission was unacceptable and the university had overstepped the line.
Barlow-Groome said she wanted an explanation as to why Scott entered the flat.
Critic reported a university spokeswoman saying the proctor was comfortable with the action taken".
The proctor spoke to the male occupants in the flat and made them aware of the action that was taken, with the flat occupants acknowledging the equipment had been used to smoke cannabis. The bongs all contained cannabis residue and have been disposed of.
The action comes after hundreds of copies of the Critic's "Menstruation issue" - featuring a naked person menstruating on the cover - were taken by Campus Watch overnight earlier this year, hitting headlines nationally and internationally.
The university later said taking the magazines was a mistake made by someone working in the proctor's office.
The proctor is not a police officer, and it appears the university's code of conduct does not give the proctor the ability to enter private homes without permission.
Abe Gray, cannabis activist and owner of the Whakamana Cannabis Museum, told the Otago Daily Times he understood correct police procedure would be to send the bongs for forensic testing and establish they had been used for cannabis before prosecuting their owners.
Comment has been sought from police.
The Whakamana Cannabis Museum has offered to sponsor brand new water pipes for the flat.
