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The roof of the former NZR bus station building will be replaced this year as part of the $35 million redevelopment, requiring the archives to be packed away for safekeeping.
The archives have about 1000 users each year.
Museum staff said photographs in the museum's portrait gallery could be seen there as usual, and about 6000 portrait photographs from the archives had already been digitised and would soon be made available via computer.
Museum director Linda Wigley said details of how the digital images would be accessed had yet to be determined.
Museum officials said it was likely at least some material would be provided via a national museum internet site.
Some other parts of the settlers' museum would be closed to the public from time to time during the redevelopment.
Some other information would be made available via computer.
Ms Wigley said the archives were closed to the public on December 24 last year.
She regretted any inconvenience, but said it was necessary to protect the safety of both the archives and the public.
"We want to minimise the disruption, but it's going to be a building site and we have to close certain areas."
While staff were still available and would help as much as they could with queries, some of the archives would not be available.
Redeveloping the archives and research facilities was essential "if we are to improve access to our archive holdings and meet the demands of an increasing number and variety of users", she said.
After 2012, the new archive would be more than twice as big, and better than the previous facility, offering greater access and space for researchers and collections.
The new facilities would offer a new research archive and stack, and a "hands-on" computer facility, where visitors, particularly school children and students, could search the archive and download information from the museum's database themselves, without necessarily handling original material.
The Dunedin branch of the New Zealand Society of Genealogists has recently been packing up parts of its own archives library, long housed rent-free at the museum.
Early next month, that library will be shifted to new rented premises at King Edward Court, the former King Edward Technical College complex, in upper Stuart St.
Branch secretary Janet Rutherford said that the library would reopen for branch members mid to late next month.
Members had initially been surprised about having to move out of the museum, but the branch had been given about three months' notice, which was a "reasonable" time to find alternative accommodation, although this had proved difficult, Mrs Rutherford said.
Branch members would not be inconvenienced by the museum archives' closure, with continued access to the branch's own facilities, as well as resources at the Hocken Library and Dunedin Public Library, she said.