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The ferry, also called the Tuapeka Mouth Punt, is funded by the Clutha District Council under its road maintenance contracts and is treated much like a bridge. Use of the ferry is free.
Council district assets manager Jules Witt said operation of the ferry was initially suspended on January 10 because of flooding and high flows on the Clutha River.
It was later suspended further as a result of damage to the ramp anchor point on the Tuapeka Mouth side.
Planned maintenance and repairs to the ferry had been prioritised under the council's bridge repairs contract for the 2012-13 year, which was awarded to SouthRoads Ltd, he said. The ferry was expected to resume operating late next month.
The contract includes repair and maintenance work to the ferry, including replacing the timber deck and handrails on both ramps, replacing steel beams on one ramp and construction of a new anchor system.
The repairs had been given priority under the contract to ensure the ferry was operational again as soon as possible, Mr Witt said.
A riding trail of the Otago Goldfields Cavalcade was due to use the punt next Thursday, but had to alter its plans.
Gambler's Last Hand trail boss Stu Moore said it was disappointing the trail would not be able to use the ferry service.
''It's a shame - it [the punt] was part of the spin on the ride.''
Horses would be transported from the Rongahere punt site to Tuapeka Mouth by horse float, and would carry on as planned, riding from Tuapeka Mouth to Tapanui through the back of the Blue Mountains, Mr Moore said.
The Tuapeka Mouth Ferry is about 30km northwest of Balclutha. It normally crosses the Clutha River daily between 8am and 10am, and 4pm and 6pm. The New Zealand Transport Agency funds 60% of the punt's costs.
The historic punt was used mainly as a tourist attraction, but some locals also used it on a regular basis and Mr Witt apologised for any inconvenience caused.