The government has accused foreign and local non-government organisations (NGOs) working in the embattled north and east provinces of helping the Tigers with logistics, a claim the charities deny.
"The defence secretary has had discussions with NGOs and got their consent to investigate any NGO which the government suspects of helping terror activities," Rambukwella, who is also the foreign employment minister, told reporters.
"The NGOs have agreed to this, and we are also giving them a chance to present their side of the story in order for them to clear their names," he said.
"We also have the right to request them to pack up their bags and leave, in the event they are found guilty," he added.
The move follows the killing of 17 local aid workers belonging to French charity Action Against Hunger (Action contre la Faim) last August in the northeastern town of Muttur.
They were shot in the back of the head at their offices.
Scandinavian ceasefire monitors blamed the military fo