A refugee advocate speculated the raid was undertaken to make way for any visa defaulters nabbed in the Melbourne CBD in the infamously cancelled Operation Fortitude.

But that claim was emphatically denied by an Immigration Department spokesman who said the operation was a routine search for unauthorised and illicit contraband.

"The Department can confirm a number of detainees were recently transferred within the detention network, as part of a pre-planned move," said the spokesman.

"The searches conducted at the MIDC on Friday were not linked to the transfers. For operational and security reasons we cannot comment further."

According to one source, a team of up to 70 officers from the ABF, its dog squad and Serco Emergency Response Team swooped on the centre at 2.30am.

They are believed to have woken the detainees, handcuffed them and put them on buses bound for chartered flights.

The men, some of whom are asylum seekers, were then taken to an undisclosed location.

Fairfax Media understands they were en route to Yongah Hill Detention Centre, north-east of Perth, and Christmas Island Detention Centre.

The ABF officers and Serco ERT team then continued to search each of the remaining 90 detainees –including 10 women – and their rooms until 5.30pm on Friday.

The source, who did not want to be named, said there were "distressing scenes" at the centre, with the men "screaming" while being forcibly removed.

The detainees were "terrified" of being taken to Christmas Island as they would be cut off from their friends and family, he said.

"There is an atmosphere of fear and intimidation at the centre now," he said.

"One of the detainees said 'we are treated like dogs'."

Asylum Seeker Resource Centre detention rights advocate Pamela Curr said the families and friends of the detainees had been unable to find out where the men were taken.

"We have got people contacting us now, asking us to find their loved ones who have been moved effectively to a secret prison," Ms Curr said.

"We have gone from secret on-board matters to secret in-detention centre matters where people are being moved from detention centre to detention centre in the middle of the night and their family members are not allowed to know where they are going."

She believed the government removed the detainees in a bid to "make room" ahead of the cancelled Operation Fortitude, she said.

"This was the day they announced the visa inspection program in Melbourne," Ms Curr said. "What they would have been doing is clearing out the Maribyrnong Detention Centre with hopes that they could pick up visa anomalies and whack them into detention.

"We don't know that [for sure] but it is the most logical explanation."

However, a spokesman for the Department of Immigration and Border Protection said the raid was conducted to ensure the safety of the centre and "stamp out criminal behaviour".

Similar operations would continue on an ongoing basis, he said.

"The key message is we have a zero tolerance to illegal behaviour in our centres," the spokesman said.

"A variety of contraband items were seized during the operation, including drug paraphernalia and a homemade tattoo gun."

When asked if any criminal charges had been laid, the spokesman said "detainees found in possession of illegal contraband may face criminal charges".

The raid followed "success of Operation Safe Centres in March earlier this year" and was conducted to ensure the "safety and good order of our Immigration Detention facilities centres, while identifying detainees who are doing the wrong thing", he said.

However, a source told Fairfax Media the officers found only "two glass smoking pipes", "Iphones" and "trolleys upon trolleys of extra linen" and extra mattresses that the detainees had amassed during their stay at the centre.

"No drugs were found," he said.

"In a search lasting all day, almost 80 officers searching 90 detainees and all they find is a tattoo gun and a couple of glass bongs?"

"It was an overkill."