The chargesheet was filed before the NIA Special Court in Visakhapatnam in the first chargesheet of the case, officials said.
All three accused have been booked under provisions of the IPC, the Explosive Substances Act and the Unlawful Activities (Prevention) Act.
According to the agency, two of the accused, Nama David Raj alias Deveedu and Vijay Viswas, were identified as overground workers of the CPI (Maoist).
They were allegedly caught red-handed and arrested by local police while en route to deliver a consignment of explosives to the third accused, Sodi Kesa, an underground Maoist cadre.
NIA investigations reportedly revealed that David and Vijay were involved in the procurement, transportation and supply of explosive materials to underground Maoist operatives.
Officials said the agency found that the alleged conspiracy was aimed at strengthening the operational capabilities of the CPI (Maoist) to carry out attacks on security forces and disrupt internal security.