Sources say, all the three states have increased vigil on international and inter-state borders.
"Security along the borders will be further tightened in view of the counting of votes," an election commission official.
There is a directive from the union home ministry asking the states to take steps to seal the international border by deploying additional Border Security Force and Assam Rifles troopers.
The BSF guards India's border with Bangladesh while Assam Rifles is posted along the Myanmar border.
Four northeastern states -- Tripura, Meghalaya, Mizoram and Assam -- share a 1,880-km border with Bangladesh. Mizoram, Manipur, Nagaland and Arunachal Pradesh share a 1,640-km border with Myanmar.
Most of the international border is unfenced and runs through dense forests and mountainous terrain, making it porous.
The official said the poll panel has asked the states to ensure three-tier security around the counting centres.
Central paramilitary troopers will be posted inside the counting centres, while other security forces will guard the outer areas.
Assembly elections in Tripura, Meghalaya and Nagaland, having 60 seats each, were held on February 14 (in Tripura) and February 23.