The State Ports Authority will pay $2.2 million to settle a land dispute over a rail yard it is building in the Upstate, adding costs to the project but minimizing the risk of missing the September opening.

The SPA board held a special meeting by telephone Tuesday to authorize the agency to pay Nordic Cold Storage to buy out the 11 years remaining on the company’s lease. The warehouse business rents part of the maritime agency’s 40-acre “inland port” site in Greer.

Jim Newsome, the SPA’s chief executive officer, declined to comment about the settlement Tuesday. He previously has said he hoped the dispute could be resolved outside of court.

The SPA broke ground March 1 on the inland port, where shipping containers will be transferred between trucks and Norfolk Southern rail cars running to and from the Port of Charleston. It’s expected to take tens of thousands of trucks off of state roads and highways each year.

The SPA board voted after the ground-breaking to force Nordic to move by condemning and demolishing its building. Lawyers for Nordic filed a lawsuit in Spartanburg County Circuit Court on April 11, challenging the plan and potentially holding up the completion of the project.

The complaint said Nordic told SPA in November that it could move, but that it would require up to nine months to find a new site. Port officials said that same month that they would be able to work around the warehouse, and that the container yard would “enhance” the company’s business, according to the lawsuit.

In February, the SPA informed the company “it needed to find a new home quickly and could not stay at the location,” Nordic alleged.

Nordic said it has been looking for an alternate site, but it had not been able to find one yet. CEO Don Schoenl was not available to comment Tuesday.

Tuesday’s $2.2 million settlement increases the SPA’s investment in the inland port by about $1.2 million, officials said. The other $1 million had been factored into the cost of the project under an earlier budget.

The deal comes just days after the board approved an additional $12.9 million for the development, or roughly 50 percent more than the original cost estimate of $33.6 million. Of that, $26.1 million was to come from SPA and a maximum of $7.5 million was to come from Norfolk Southern.

Updated estimates raised the total price tag to as high as $48.6 million, with about $40 million coming from the SPA. Officials have said the extra money is needed to speed up construction, acquire more land and add capacity.