The decision was made as joint operations are being conducted in the area against the KNF, the Election Commission said
Naogaon Sadar Police Station OC Jakirul Islam said this happened at the Naogaon bus terminal around 4:30am on Sunday.
One of the vehicles was totally gutted while the other was partly damaged.
Locals said buses that run on Dhaka-Naogaon route have been parked at the terminal since the blockade was called on Jan 5.
Fire service put out the flames after 30 minutes.
No casualties have been reported, the OC said.