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Dunedin City Council parks manager Lisa Wheeler said since the $382,000 jetty was opened in 2012, holes had begun appearing in the pontoon and repeated underwater repair attempts had failed.
The holes meant the pontoon had filled with water and was on a lean.
''When it was installed it passed all its tests ... so we have no idea what's happening,'' she said.
In an effort to identify the problem and rectify it, the council decided to have the pontoon towed into dry dock in the upper harbour, before being returned to Portobello.
Transport costs were expected to come to about $14,000, and the council was unsure about the cost of repairs.
''It just depends on what the investigation comes out with.''
The jetty would be closed while the pontoon was being repaired, which was not expected to take any more than a month.
The work was expected to be finished before summer, although its timing had not yet been decided.
The jetty - a joint effort between Portobello Community Inc, the council and other funding organisations - was officially opened in February 2012.
It was constructed by Amalgamated Builders.