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The decision to advertise the post comes about six months after previous Toitu director Linda Wigley left and after talks between the institutions about closer collaboration.
DCC arts and culture group manager Bernie Hawke noted Ms Wigley had been gone for about six months and said advertising the post was appropriate for Toitu staff and stakeholders.
The move also reflected the standing of the council-owned Toitu museum, which last year won the Museums Aotearoa ''Project Achievement Award'' after its $37.5 million redevelopment, Mr Hawke said.
Toitu acting director Jennifer Evans and Otago Museum director Dr Ian Griffin have held talks about closer collaboration between the institutions.
Museum representatives have emphasised that amalgamating the museums was not being considered.
Full details of talks have not been provided, but it is understood ideas include making savings through efficiencies, such as through some shared buying.
It is understood one option considered, but not pursued, was to maintain two separate institutions with a senior director, based at the Otago Museum.
It is understood this idea was not taken any further and was not referred to the DCC for further consideration.
Asked about this, Mr Hawke said it was not appropriate for him to comment about any such specific ideas.
Discussions had focused on ''how both museums might benefit'' from collaborating over a ''range of matters'', but amalgamation had not been considered, he said.
Some Otago Museum staff, including assets and technology manager Joel Oldridge, have provided support for Toitu in some areas, including aspects of maintenance, after former Toitu facilities and services manager Damian Mallon left when his contract came to an end.
Ms Evans said she was enjoying the improved relationship between the museums.
Otago Museum marketing and development manager Caroline Cook said closer links would bring significant benefits.
Toitu board chairwoman Dr Dorothy Page welcomed the decision to advertise the director's post and said it was appropriate for the museum to have its own director.