CANBERRA, June 12 (Reuters) - Australia's largest sugar producer halted operations on Wednesday at a mill that began processing cane two days ago, after unions agitating for better pay said workers would lay down tools, the company said.

The mill in the northeast Burdekin region is the only one of eight run in Australia by Wilmar Sugar and Renewables that has begun its cane crushing season, with the others due to begin operating in the coming weeks.

The start of processing at all eight mills was delayed by the pay dispute, which poses an increasing threat to Australian sugar production and exports as it could shorten the crushing season and cause cane to be left unharvested.

Workers rejected a pay offer in a vote that ended on Tuesday and are conducting short-term work stoppages and bans, the company said.

"The only sugar mill operating in the Burdekin, Inkerman Mill, has been forced to shut down overnight after union delegates advised that workers plan to stop work at that site, and at least two other sites, for one hour at midday today," Wilmar said in a statement.

Operations manager Mike McLeod said the company had decided to stop the mill for operational and safety reasons because it was unclear whether workers would stop work again on Wednesday.

"A safe shutdown usually takes about 12 hours and must be carried out with care and precision, he said.

"We must now consider whether we can proceed with our expected start at Invicta and Kalamia mills later this week," McLeod added.

The cane crushing season on Australia's hot and humid northeast coast begins in June and runs to around November.

Wilmar Sugar and Renewables produces over 2 million metric tons – worth around $1 billion - of sugar a year, over half of Australia's total production. It is owned by Singapore's Wilmar International.

The company has offered workers a 14.25% wage increase over 3.5 years and an A$1,500 ($1,000) sign-on bonus. Unions are asking for 18% over three years.

($1 = 1.5135 Australian dollars) (Reporting by Peter Hobson; Editing by Sonali Paul)