Brigadier General Elias Zamani said that armed youths had moved into the area to protect Diepreye Alamieyeseigha, the state's governor, and he feared that fighting could break out unless the troops were deployed.
"The area has been tense, there have been attempts by the house for impeachment," he said. Militant youths have been moved into that place armed with weapons.
"There are different groups. The way things are going it could escalate to where different groups start fighting. So it's a pre-emptive step to save lives and property."
Soldiers on Monday morning set up road blocks and searched vehicles in Yenagoa, the Bayelsa state capital.
Bayelsa produces a quarter of Nigeria's 2.4 million barrels per day of oil output.
Alamieyeseigha fled money-laundering charges in London this month and returned to Nigeria where he has immunity while in office.
The state house of assembly has begun impeachment against him, but the motion is unlikely to achieve the two-thirds majority required to pass.
Alamieyeseigha has accused the federal government of trying to cause mayhem in the state as a pretext to impose a state of emergency, which would strip him of his powers.
Another military official said the governor, who is a self-styled champion of the Ijaw ethnic group dominant in the southern Niger Delta, was using militant youths dressed in military uniforms to protect him since his police escort was withdrawn.