No casualties were reported after drivers fled for their lives when a brake-lining fire apparently caused the 15-tonne commercial truck to burst into flames inside the tunnel, they said.
A convoy of four trucks was carrying two dismantled missiles, the air force said.
Two leading trucks carrying missile warheads had just passed through the tunnel when a third truck in the convoy burst into flames, they said.
Occupants of some 50 cars fled to safety as smoke billowed from the 1.5 kilometer (one mile) tunnel.
"There were no casualties," Daegu Fire Department official Kyong Soo-Hyun told AFP. "There are some 50 cars still stuck in the tunnel. But motorists all evacuated the tunnel upon the fire."
The air force said the convoy was carrying two ageing Nike Hercules surface-to-air missiles that had been dismantled and were being replaced by new US Patriot missiles at a south-western missile battery.
The burning truck was carrying solid rocket fuel but the series of blasts was unlikely to be related to that, the air force said.
"Fire, presumably caused by the truck's failed brake system, spread to tyres and then the solid rocket fuel," an air force colonel who identified himself as Lee told AFP.
"The solid rocket fuel usually does not explode but burns."
Fire-fighters said the blasts were more likely to have been caused by vehicle fuel tanks exploding. Witnesses said they heard seven or eight loud blasts in the tunnel 300 kilometers (187 miles) south-east of Seoul.
The Ministry of Defence said it was investigating the cause of the incident in the Dalseong 2 Tunnel on the Guma Expressway which links Daegu to the coastal town of Masan.