The agency building the new World Trade Center says a design flaw could add millions of dollars to the cost of the complex's signature tower.

The Port Authority of New York and New Jersey said Tuesday that the loading dock under One World Trade Center won't be finished in time for tenants to move their equipment into the 104-story tower. So it's building five temporary loading bays above ground.

A temporary station that was built for the Port Authority Trans Hudson subway is blocking access to the underground loading area. The station can't be dismantled to make way for underground freight areas until crews finish the permanent station.

"Several years ago there was a design miss," Patrick Foye, executive director of the Port Authority, told reporters on Tuesday. "Should it have been caught? The answer is, probably."

The temporary loading bays will add millions to the cost of One World Trade Center, the glass and steel spire previously known as the Freedom Tower. The building is now 90 stories high.

"We and the other concerned stakeholders believe this will be a short-term issue and will not impede completion of the site or tenants moving into the buildings," Foye said. He spoke after giving a speech to the Association for a Better New York.

The Wall Street Journal on Monday reported that the cost of One World Trade Center has soared to $3.8 billion, $700 million more than the last publicly released estimate in 2008.

Foye said the rising costs will be examined in a review of the agency that is being prepared for the governors of New York and New Jersey. He would not confirm the $3.8 billion figure.

Other problems at the World Trade Center have included a dispute with the foundation that is building a 9/11 museum and financial troubles that have dogged the company that is laying steel.

Foye said One World Trade Center is 60 per cent leased by tenants including the Conde Nast magazine company and Vantone Industrial, a Chinese real estate company. But other buildings planned for the complex have struggled to find occupants.

Last week Silverstein Properties Inc., the developer building the 80-story Three World Trade Center, said it is still looking for tenants to fill the first 10 floors of that building, which is already under construction. If it cannot fill 10 floors, Silverstein must stop construction at seven floors under a financing agreement with the Port Authority.

The second-highest building in the planned complex, the 88-story Two World Trade Center, is also on hold because of a lack of tenants.

Foye said the Port Authority still expects to finish One World Trade by the end of 2013.

He said completion of the tower will allow the agency to refocus on its transportation duties, including long-overdue overhauls of its bridges and improvements to its airport terminals.

Tuesday was the deadline for contractors to send proposals to the Port Authority to replace La Guardia Airport's Central Terminal, which Foye called obsolete.

"It's got a quaint, nostalgic but unacceptable kind of 1940s, 1950s feel that's just not acceptable," he said.

Foye also said about $350 million is earmarked for overhauling Terminal B at Newark Liberty International Airport. Travelers have criticized that terminal because of the way it limits passengers to individual "piers" instead of allowing them to move around the whole terminal.

Later this year, the Port Authority will also ask contractors for proposals to build a new Terminal A at Newark, Foye said.

Delta Air Lines and the Port Authority are also renovating Delta's hub at John F. Kennedy International Airport's Terminal 4, mostly through $900 million in special-project bonds.