The heat from layers of lava and ash melted the troops' shovels, and work was frequently disrupted on Thursday as they fled from plumes of blistering clouds rolling down the slopes of the volcano on Java, a disaster official said.
By nightfall, the soldiers with the help of two mechanical diggers had unearthed debris surrounding the door of the bunker, but found it blocked by a large, hot boulder, the official said. The operation was suspended until dawn on Friday.
It was unclear if the men were still alive in the bunker, which is one of many dotted around the slopes and built to protect rescue workers from eruptions. The men are thought to have been helping to evacuate villages when they took shelter.
Merapi continued to spew out scorching gas clouds and rock fragments on Thursday. One black plume in the afternoon covered a large swath of the mountain. No injuries or fresh property damage were reported.
Scientists had thought that Merapi, which is 3,000m high, was calming down after weeks of activity, but violent eruptions on Wednesday led to villages in the area being evacuated again. The Indonesian government has put the volcano back on its highest alert level.
Antonius Ratdomopurbo, a vulcanologist, said the resurgence in activity was probably caused by the collapse of a section of lava dome, which had been growing in recent weeks as lava emerged from its core.
The main dangers at Merapi are fast-moving bursts of hot gases and rock fragments called pyroclastic flow. Scientists at the site say that a massive vertical eruption, which would threaten people many kilometres away, is very unlikely.