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The 12 Ontario poplars were removed from alongside Logan Park Drive in September last year, in part to address shading problems at the neighbouring University Oval cricket ground.
But, following complaints from a member of the public, council infrastructure and networks general manager Ruth Stokes on Friday conceded the council's oversight of the project ''fell well short of expectations''.
Her comments came after Dunedin man Bob Gillanders, the retired farmer behind a green waste disposal business at Burnside, raised concerns about the cost and council processes.
He told the Otago Daily Times the $32,500 charged by the council's contractor, Asplundh, appeared to be double what it should have been.
The company should have been paid no more than $15,000, based on his own experience and knowledge of the industry, Mr Gillanders said.
Asplundh's invoice included some ''pretty eye watering'' charges, including $20,000 for the removal of the trees, and traffic management and other associated costs.
''That's just ridiculous; absolutely ridiculous.
''I know what all this gear costs to hire ... I'm familiar with this stuff, and these people [council staff] aren't.''
Asplundh Dunedin area manager Alan Page declined to comment yesterday, but Mrs Stokes accepted the council's handling of the contract was ''not ideal''.
Mrs Stokes, in an email to Mr Gillanders, said the council had not followed ''normally applicable processes'' in commissioning the work.
The price was ''at the high end'' of what could be expected, which was ''not to say I am happy with the price paid'', she wrote.
Work specifications had also been issued verbally to Asplundh, the council's tree maintenance contractor, rather than council staff seeking three quotes from separate companies, she said.
That was the result of ''a new staff member with inadequate management oversight, and I agree that this particular procurement fell well short of expectations'', she wrote.
''I have discussed this with the staff concerned.''
Mrs Stokes, speaking on Friday, told the ODT the problems were similar to those encountered over the South Dunedin cycle network.
A ''massive amount of work'' had been undertaken since then to improve the council's handling of parks contracts and ensure problems would not be repeated, she said.
''Staff were busy beavering away and there wasn't the appropriate senior management oversight over how things played out.
''We're in a completely different world now, and that's changed significantly.''