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The 33,000-tonne Singaporean-flagged vessel has been the subject of protests in recent weeks for carrying 51,000tonnes of controversial phosphate rock from Western Sahara.
It was believed to have struck part of the Ravensbourne wharf as it berthed last Wednesday.
Maritime Union of New Zealand Port Chalmers Dunedin secretary/treasurer Phil Adams said concerns over possible structural damage and the safety of those unloading the vessel prompted the union to stop its members from working on the wharf .
"One of our members rang me and said that they didn’t feel the wharf was safe until it had been checked out.
"So they went home on that note."
The wharf was checked on Thursday last week and was found to be structurally sound, so the workers went back to work.
Port Otago marine and infrastructure general manager Sean Bolt said the incident was "not a big deal".
"It didn’t really strike the wharf.
"A couple of steel bracing rods [between the piles] underneath the wharf broke when the tug was pushing on the vessel."
One of the rods had already been repaired and the other would be repaired tomorrow, he said.
While the incident did not delay the unloading of the vessel, high winds had slowed the process on Friday.
The vessel was expected to move to the Beach St wharf this morning before departing on Wednesday.
Federal Crimson has already visited the Ports of Napier and Lyttelton, where it was met with protest.
Ravensdown Fertiliser worked hard to stave off similar action in Dunedin.
Much of the world's phosphate supplies come from Western Sahara — a piece of desert land about the size of New Zealand.
It was a Spanish colony but was taken over by Morocco in 1975, and has been a bitterly disputed territory ever since.
The international Council of Trade Unions recently condemned Morocco’s illegal occupation of Western Sahara and resolved to halt importation of phosphates from the area into New Zealand.
Ravensdown has acknowledged people’s rights to protest, but said the trade was legal, complied with United Nations expectations and was welcomed by the Saharawi who were employed at the mine the phosphate comes from.