Sea Horse Sea Freight's Allison Lozell said the firm will be ready to begin bringing horses back across the Tasman into Auckland, Tauranga and Timaru as soon as the current five-week quarantine requirement is lifted.
MAF Biosecurity has sought public submissions on a new import standard for horses from Australia, which proposes ending quarantine requirements.
Submissions close on December 22 and quarantine-free horse movements from Australia should be under way by the end of January at the latest.
Lozell said new containers were under construction to increase the firm's capacity and she confirmed a new service would be available from Melbourne to Timaru.
The service would save South Island horse owners $600 or more in road transport costs from the North Island, she said.
She expected the cost per horse would be around $NZ3200 to cross the Tasman.
She had hoped to keep the cost to $NZ3000, but said sea freight was paid in United States dollars and the New Zealand dollar had fallen against the greenback.
She had yet to determine the full extent of the backlog of horses to be cleared.
"Some people have sold their horses [in Australia]. A few have flown them in. Some now have foals. I couldn't give you a precise figure," she said.
The new containers will bring the firm's total to six, with each capable of holding six horses. The maximum number of horses permitted on any one sailing is 24.
She said she had a dozen horses ready to go into the South Island and would run that service whenever there were six horses bound for the south.
She said containers would be relocated to Australia in preparation for bringing horses into New Zealand.
Normally, she said, the firm would send full containers both ways but, for a time, empty containers would have to be shipped back to Australia to help clear the backlog.
She said the firm has been running at about 50 per cent capacity since the equine influenza outbreak in Australia which began in August last year, which brought the trans-Tasman trade to a halt.
"This year we have exported to nine different countries," she said.
For a time following the flu outbreak, hardly any horses were sent to Australia, with owners fearful of horses being stuck in transit as a result of the widespread movement lockdown.
The last case of equine influenza in Australia was on Christmas Day, in Queensland. Under formal international guidelines, Australia cannot be considered formally free of the disease until a year after that date.
New Zealand re-opened its borders to horses from Australia in mid-May, but horses required three weeks of quarantine in Australia and two weeks here.
However, quarantine facilities were available only to those opting to bring horses in by air. The cost, including quarantine, was around $10,000 a horse.
Before the flu outbreak, Sea Horse Sea Freight was charging $2600 for importing horses out of Sydney, Adelaide and Melbourne, with Brisbane being a little dearer.