The spread of the varroa bee mite to southern parts of the South Island means some beekeepers will struggle to remain profitable this season.

The parasite, which kills unprotected bee colonies,  is now embedded in Canterbury after spreading from the North Island.

Federated Farmers' bee group chair John Hartnell says it costs beekeepers between $20 and $50 a year per hive to control varroa.

He says the extra costs are likely to hit South Island honey producers harder than their northern counterparts.

Estimates say up to 70% of pipfruit and summerfruit orchards in Central Otago are pollinated by feral bees and the orchardists have never paid for commercial pollination.

But John Hartnell says there could be further opportunities for South Island beekeepers to provide pollination hives in the next few years.