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Dr Clark said documents released under the Official Information Act, which show officials scrambling to respond to an impasse over a long-term lease for the pool, suggest a lack of leadership from Health Minister Jonathan Coleman.
A community campaign backed by the Otago Daily Times raised $1.2 million for an upgrade and running costs for the historic pool.
The upgrade was supported by the former health board - which was sacked a year ago - but was put off at late notice last year because Wellington officials feared granting a long-term lease could compromise Dunedin Hospital development plans.
The pool is on the hospital campus, and officials are keeping their options open for the planned $300million rebuild of the hospital.
The papers show Southern District Health Board senior managers were keen for a lease to be granted as recently as six months ago.
"The success of the trust's fundraising campaign gives weight to the community view that ongoing operation of the pool is desirable. The issue is highly sensitive in the community,'' said a report by Peter Beirne, who no longer works at the board.
It is unclear why the problem was not signalled earlier, given the redevelopment had been in the offing for a significant length of time.
A decision on the lease is not expected until the middle of next year, which creates difficulty for the Otago Therapeutic Pool Trust because of time limits attached to some funding grants.
Officials have proposed a "letter of intent'' to show funding bodies to protect the grants, and the trust is now pursuing that option.
Dr Clark said it was not good enough.
"The pool is located across a state highway [from the main part of the campus] and it is obvious that it won't interfere in any meaningful way with the rebuild.
"They are putting an imaginary risk ahead of the health and wellbeing of elderly and vulnerable Dunedin residents.
"It looks like bureaucracy and backside-covering is putting all the hard fundraising work the trust has done at risk,'' Dr Clark said.
He said Dr Coleman should step in to ensure the pool trust was able to proceed with its long-signalled upgrade.
Pool trust secretary-treasurer Neville Martin said a letter of intent, while not his preferred option, could bridge the gap until the decision.
"The letter of intent would serve as a tool to attempt to keep organisations which have offered grants for the upgrade informed and supportive.
"The letter would be a positive signal, but nothing more, and would not enable the upgrade to proceed.''
Emails released under the OIA show Ministry of Health officials were working "urgently'' to resolve the problem.
"An answer to this will be difficult,'' one senior ministry official told colleagues.
Dr Coleman's office did not respond to questions before deadline last night.