After months of design and engineering alterations aimed at cutting costs, the Port Authority has been unable to fully rein in expenses at the Santiago Calatrava-designed PATH Station planned for the former World Trade Center site. Despite several structural and design changes, the agency will be left with up to $300 million in overruns, according to people familiar with the plans.

Earlier this year, the Port Authority received estimates that showed the transportation hub could cost $1 billion more than the $2.2 billion that was budgeted.

The agency, controlled by commissioners appointed by the governors of New York and New Jersey, is now finalizing a plan for the station, which is expected to serve 80,000 PATH riders a day.

The new PATH station, a soaring, skeletal structure punctuated by white spires that is meant to represent a bird in flight, is one of the last major unresolved projects at ground zero. Construction of the Freedom Tower is under way, and the Port Authority has said early site preparation for the three other office towers at the site is on schedule. While the World Trade Center Memorial was forced to trim costs significantly last year, reducing its budget to about $500 million after estimates showed the price tag could hit $1 billion, the memorial is now moving forward and has nearly reached its private fund-raising goal of $350 million. Given the changes worked out in recent months, the amount of the overruns will be less than $300 million, according to one Port Authority official. A spokesman for the agency, Steven Coleman, said the designs of the PATH Station have not yet been finalized.

“This is still a work in progress and there’s been no final decisions made,” Mr. Coleman said.

In proposing any changes, particularly alterations that would affect the design of the station, the Port Authority is said to have met resistance from Mr. Calatrava, a world-renowned Spanish architect whose works were exhibited at the Metropolitan Museum of Art between 2005 and 2006.

Most notably, Mr. Calatrava has successfully fought to preserve a function for the station’s roof, which would open and allow light to stream inside the concourse below, people with knowledge of the discussions said. Given the expense and relatively limited use of the function, the ability of the roof to open was seen as an early target for potential cost savings.

The changes to the project would be both seen and unseen, sources said, as the Port Authority altered aspects of the structure’s engineering, but also pursued more noticeable changes to retail area and pedestrian access.

Despite the substantial cuts to the project cost, the overruns would leave the Port Authority paying far more than it anticipated for the project: to date it has only committed $300 million. The other $1.9 billion in the budget comes from the Federal Transit Administration, which is viewed as an unlikely source for any additional funding. A city official said the Bloomberg administration has no plans to fund the transit hub.

The high cost estimates for the station, first reported in February, were not all that surprising given the complex nature of building in the World Trade Center bathtub, the president of the Building Trades Employers’ Association, Louis Coletti, said.

“It’s a complicated site,” Mr. Coletti said. “You might have to spend more money to shore up the slurry wall than was originally anticipated. There’s always — in jobs — unforeseen costs.”

The PATH trains now serve out of a temporary station, built in 2003. The first entrance for the temporary station was razed earlier this year, and its adjacent substitute, located by the northeast corner of ground zero, will soon be replaced by a third temporary entrance on the north end of the site.