The gold was seized by a bailiff on behalf of the miners at the main airport in the capital on 7 October.
But London-listed Avocet Mining,says it needs the smelted gold back to raise money for the workers' settlement.
The dispute at Inata mine dates back to 2014 and the sacking of 317 workers.
Other workers at the mine, which is about 250km (150 miles) from the capital Ouagadougou and is run by subsidiary company Belahouro, are also in dispute with the management over the payment of bonuses.
"We appeal to the justice system to be extremely vigilant. We have heard SMB-Inata is using dubious means to try to get the gold back," said Saidou Sinare, a spokesman for the sacked workers.
London-based Avocet CEO David Cather told the BBC payments to workers had been agreed and operations had resumed because the company believed the dispute had been settled.
"But we're still waiting for the gold to be handed back," he said.
"We have agreed to make an interim settlement of 565m CFAF ($1m) to the workers. This will have to come from the sale of the gold they are holding," he added.
Discussions were still under way to secure the release of the gold, the company said in a statement.
The gold is smelted at Inata and flown to South Africa's main city, Johannesburg, for refining.
The mine produced 2,120 kg of gold last year, Avocet said.
Gold mining has boomed in several West African countries in recent years.
In addition to mines run by established companies, many informal mines have opened and have attracted thousands of people who work in hazardous conditions.
Miners in Burkina Faso have seized 43kg (94lb) of gold worth about $1.7m (£1.4m), a firm says, and are refusing to return it until they get a pay-off.