Many of the Katherine Civic Centre's tall trees will be chopped.
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Mayor Fay Miller said making the decision to remove 54 trees "makes me sick to my stomach".
Two of the alderman last night opposed the move, voting against the decision to immediately move on the trees.
Deputy mayor Elisabeth Clark said council had no choice now it had an arborist's report saying the trees were unsafe.
"We would be liable if anything happened," she said.
Council was told that attacks from destructive corellas, termites and a poor wet season had combined to hollow out many river red gums in particular.
"This is the most depressing thing I have read for a while," Mayor Miller said.
"The tops of the trees have been decimated by these birds.
"I am not happy about it and I don't want that many trees to go."
Alderman Clark said council did not have a choice.
"It is sad because they do look nice."
Alderman Jon Raynor questioned whether the trees could be removed in stages.
Mayor Miller said she would rather remove all the dangerous trees as once "and get it over and done with".
Alderman John Zelley said he opposed the move and wanted a second expert opinion.
"This is just one arborist's opinion," he said.
"Other trees in the area have had similar damage and are coming back.
"They have had white ant treatment ... we may be able to salvage them."
Mayor Miller said could could be in a "terrible spot" if it didn't act on the report.
Council voted to proceed with their removal with Aldermen Raynor and Zelley voting against.
The removal of the trees is estimated to cost about $20,000.
Council was told officers are already in the process of planning for a replanting program.
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