"We have launched an investigation and anyone breaching discipline will be dealt with," Brigadier Jayanath Jayaweera, the Army spokesman said.
The incident caused a furor after the white van in which the three soldiers, wearing civilian clothes, were travelling was confiscated yesterday at Mirihana, a Colombo suburb where Rajapaksa lives.
Rajapaksa's camp had raised concerns if the detection had anything to do with a possible assassination attempt on Rajapaksa's life who is hated by the LTTE supporters for his military campaign which crushed the feared terrorist organisation.
However, Jayaweera said that the vehicle belonged to the Army and why it was carrying false registration plates would be investigated.
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Jayweera also added that the arrested soldiers were having a firearm issued to a Major General.
The Rajapaksa government has been accused of deploying white vans to intimidate opponents, media and civil society.
Many abductions by groups in white vans were repeatedly reported while no proper investigations were conducted, human rights groups charged.