The wharf structure was scheduled to be replaced in 2015, but work on rebuilding and repairing the ageing structure began last April.
Candide Reid, who co-owns Raglan Kayaks, lost her business and all of her belongings in storage there during the blaze.
She said the higher rent costs meant it was unlikely her business, which runs between Labour and Queen's Birthday weekends, could return to the wharf.
"I would have loved to have gone back to the wharf, but it's not sustainable for us.
"We heard the price of rent would increase amazingly. I'm not sure how much but it won't be as cheap as it was before. It's a shame because we were creating a really beautiful space in there. It was slowly getting there and more and more people were going there."
Mark Mathers, who owns Raglan Seafoods and provides about 200 tonnes of fish to Auckland businesses each year, said he would occupy two spaces at the new wharf. But his rent had almost doubled.
Local resident and former Raglan tourism chairwoman Rosie Worsp was fearful the high rents could turn the new wharf into a $2.9 million white elephant by keeping other businesses away.
"It was humming along and was starting to develop a bit of character ... My fear is that it could become cheap and tacky."
But another local businessman, Charles Young, said despite the lack of tenants it was early days and he still believed the wharf would be a success.
"Obviously as a business owner you want to see things vibrant and successful and I still believe the wharf project ... will be that.
"I think people want to see the final product there and it is still too early for businesses to make a commitment to the wharf without seeing the finished project."
Waikato District Council water and facilities general manger Richard Bax said the council-approved contract value for the construction was $1,943,200 but the total project cost - including the design and the repair work undertaken to the wharf - was $2,893,570.
He said that as a result, rents were higher to reflect the cost of the new building and "current market leases" in Raglan, which had been established by an external consultant.
Mr Bax said there was less space in the new building for seven tenants as the council had to comply with legislation requiring toilets inside.
Rodger Gallagher, who runs The Raglan Website, said an economic impact study he had completed estimated the loss of the wharf cost the town $3 million a year.