By Carl Odera

JUBA (Reuters) - Gunfire erupted inside the main military barracks in the South Sudanese capital Juba on Wednesday, a Reuters witness said, in an apparent pay dispute almost three months after fighting between soldiers in the city sparked a broader conflict.

The body of a government soldier lay in the street outside the military headquarters and a column of smoke billowed into the sky from inside the compound, sending panicked residents running through the streets.

"We're fighting over money," one soldier shouted from the entrance of the Jebel barracks as gunshots rang out.

In an effort to restore the battered confidence of donors to Africa's newest nation, the government is rolling out a payment system that requires troops and civil servants to be paid in person to ensure wages are not paid to "ghost" workers or to those who don't turn up.

The unrest appeared to be confined to the barracks, although government forces swiftly deployed in heavy numbers in surrounding streets, setting up roadblocks.

Thousands of civilians have been killed in an almost three-month-long conflict between the government forces of President Salva Kiir and rebels loyal to Riek Machar, who Kiir sacked as his deputy in July.

Although Juba has been largely calm since fighting first broke out among rival groups in the presidential guard in mid-December, rebel threats of an eventual assault on the city have left many anxious.

(Reporting by Carl Odera; Writing by Richard Lough; Editing by George Obulutsa and Hugh Lawson)