The protesters said that they entered Swan Island Defence establishment near Queenscliff before dawn on Thursday to "disrupt" preparations for impending Australian military strikes on Islamic State in Iraq.

Police spokesman Sergeant Kris Hamilton said police were aware of planned protests at Swan Island. He said protesters who breached the island just before 7am would be charged with "Commonwealth trespass".

"Police will continue to monitor the situation and will respond accordingly to ensure community safety," he said.

One of the group, Greg Rolles, 32, said they had wanted to find out more about the secretive military base and planned to hold up banners and placards.

They had been walking the grounds for a few hours before soldiers spotted them, when they split up into pairs and headed in different directions.

Two men in plain clothes saw from a great distance: "So I put my hands up and called out 'We're non-violent peace activists' or something to that effect."

Mr Rolles said he was tackled to the ground, stripped naked with a bag was placed over his head. His hands were tied behind his back and his ankles were bound.

Mr Rolles, who was in the Australian army for two years before he left in protest against the Iraq war in 2003, described the arrests as "heavy-handed and over the top."

He said one man slapped him when he didn't answer questions about the other protesters "quickly enough".

"They didn't leave bruises ... they pushed on pressure points, leaned on my ankles and shoulders, anything to cause a bit of pain," he said.

Police interviewed Mr Rolles when they arrived and escorted him off the island. He has not made a formal complaint about his detainment, saying the group was seeking legal advice.

He said he was initially fearful: "My second thought was what are they doing overseas with no accountability? How many enemies have we made?"

A spokeswoman for the Department of Defence confirmed that defence members detained four of the protesters. Victoria Police detained four others, she said.

The Defence spokeswoman would not comment on protesters' allegations they had been assaulted and threatened.

"The Department of Defence respects the democratic right of all Australians to express their views, provided this is done in a peaceful and law-abiding way.Under the Defence Act, ADF personnel have the powers to detain persons they suspect are trespassing on Defence land," she said.

"As the incident is a matter for Victoria Police, it would be inappropriate for Defence to provide further comment at this time."

The protesters were part of a larger group that held a planned blockade at the entrance gate to the island this week, which police attended.