Thomson and his cameraman spent four days in the Egyptian capital before being pulled out yesterday amid increasing attacks on the media.
"We arrived on the Wednesday and all hell was breaking loose," Thomson told New Matilda.
"We narrowly escaped [Tahrir Square] with our gear and ourselves on Wednesday."
The SBS crew were originally staying in the Hilton right on Tahrir Square along with the other foreign media, but Thomson says the hotel was "surrounded by pro-Mubarak thugs" and he was unable to do much from there.
"We were holed up in the hotel on Thursday. They didn’t want us to film from balcony — the hotel was surrounded by pro-Mubarak thugs and they were worried they were going to storm the building."
Thomson says they sat it out for a while, hoping things would get better. But on Friday he decided to move with a group of other journalists, including Channel 10’s Hamish MacDonald, to a hotel near to the Australian embassy.
From there, however, they were unable to travel back to the protests. "There were vigilante roadblocks all around Cairo. They prevented us from getting back [to Tahrir Square]. Hamish MacDonald from Channel 10 went out on Saturday and got pulled out of his car."
MacDonald was dragged from his car by the Army and interrogated, before being released. He has detailed his experience in a story for the Sydney Morning Herald today.
There have been other attacks on Australian media too.
Thomson said Channel 7 decided at the last minute to stay on at the Hilton on Tahrir Square — and that cameraman Rob Brown had since been pulled from a taxi at knifepoint. "He was rumbled into another car and handed over to the military," Thomson told New Matilda.
It was after this that SBS decided to pull its crew out. "The Channel 7 incident was the last straw, and they pulled us out."
"The embassy expected us to come out on Friday when we moved hotels but I didn’t want to." But in the end Thomson says he was simply unable to do his job.
"By the end of the four days we were one of the only crews that hadn’t had something happen to us."
Thomson said he thought the situation had calmed down on Sunday, and that many of the roadblocks had been lifted.
"The trip to the airport was calmer — we expected to get stopped by militia or the army.
"We employed an Australian-based security company and travelled in a convoy. Maybe they took us a way that they knew there weren’t any roadblocks, but the road to the airport was quite uneventful.
"I regretted leaving then — but the decision had been made."
He told New Matilda that much of the violence in Cairo is very clearly "in the [Egyptian] government’s hand".
"The [pro-Mubarak] violence down near Tahrir Square was so obviously government organised. It went on for a few days and they got some terrible publicity. On Friday morning they decided this was not a good image for Egypt and they put the soldiers out in force and the thugs didn’t turn out."
"They can turn it on and off like a tap," he said.
"And it’s how the Mubarak regime has always worked."