A source in the security forces said the assets that will be confiscated include 18 rai of land.
Amlo will hold a press conference about the asset confiscation today.
The move follows a joint forces raid at the Islam Burapa ponoh school on July 2, 2007, which led to the arrest of seven people for alleged involvement in bombings and instigating violence in the troubled region.
The subsequent investigation found that the school was used as a place to make bombs used in attacks throughout the deep South. The school was shut down on July 5, 2007.
In January this year, Narathiwat Provincial Court handed down death sentences to four of the seven suspects and 23-year jail terms for the others.
The school was allowed to reopen in February this year after Col Thawee Sodsong was appointed director of the Southern Border Provinces Administration Centre, in a move aimed at encouraging locals to cooperate with the authorities.
The security forces source said authorities have been keeping an eye on 75 of the more than 300 ponoh schools in the three southern border provinces, for signs of involvement with insurgents.
Meanwhile, Nazirah Hussain, the Malaysian ambassador to Thailand, said yesterday she was concerned about Malaysian flags being put up in the deep South, and had no idea why the flags had been erected.
She was referring to last Friday when 102 areas throughout the deep South experienced a spate of unrest and Malaysian national flags were hoisted across the region.
"This has nothing to do with the Malaysian authorities," said Ms Nazirah.
She said she did not think such incidents would affect the good relations between the two nations.
"Our border trade is important, so conflicts do no good to anyone. We cannot be complacent but need to cooperate further together," said the ambassador.
Pol Gen Wichean Potephosree, secretary-general of the National Security Council, said the agency has pressed for peace talks since early this year.
However, he said some parties concerned were reluctant to engage.
Some Muslim politicians have voiced concerns over the newly established southern command centre in Bangkok.
"The existing Southern Border Provinces Administration Centre has done a good job and engaged with the local people quite well," said Areepen Utarasint, former Narathiwat MP and a leading member of the Wadah group. "Having the new command centre will cast a blanket over the functioning agencies in the South."
Prime Minister Yingluck Shinawatra said she will discuss the crisis in the South with Malaysia's premier at the Asia-Pacific Economic Cooperation Summit on Russky Island in Vladivostok, Russia, on Saturday and Sunday.
The discussion should help in maintaining good relations with Malaysia, Ms Yingluck said.
Democrat leader Abhisit Vejjajiva urged the government to review the way it is handling violence in the South.
In Narathiwat yesterday, five soldiers were wounded, two critically, by a roadside bomb blast.
The explosion took place on a bridge in Ban Padador in Tak Bai district. The five military officers were patrolling the area in a pickup truck.