Naylor Love regional manager Ian McKie said steel purlins in the atrium-canopy roof of the building were damaged when the crane fell on them and needed to be replaced.
The main structure of the building was not damaged.
The 560sq m visitor centre, costing about $2 million, is being built on Blueskin Rd and is due to be finished mid-year.
Mr McKie said the crane was being operated by a subcontractor and no-one was injured in the crash, which happened about noon.
How the crane toppled was being investigated and would not be known for several weeks.
The Department of Labour was also investigating the crash.
The damage was already being repaired and the building was still expected to be completed on time, Mr McKie said.
Ecosanctuary general manager Chris Baillie referred all queries to Naylor Love.
