The Port Authority of New York and New Jersey is expected to miss the September deadline it set to turn over land for Tower 2, to be built by the developer Larry Silverstein at the World Trade Center site.

The Port Authority was supposed to turn over the site to Silverstein Properties on June 30 and since then has incurred a $300,000-a-day penalty, which it must pay the developer. Earlier this month, the Port Authority said it would turn the site over by the end of September, but according to a number of sources, that deadline will not be met.

As of the end of September, the Port Authority will have incurred $18 million in penalties for the Tower 2 site. That figure, coupled with the $14.4 million the Port Authority paid as a result of a previous missed deadline, pushes the authority’s total penalties over the $30 million threshold. If the Port Authority fails to hand over the site by the end of October, the penalties will be more than $40 million.

A spokesman for the Port Authority, Steve Coleman, said the agency still plans to turn the site for Tower 2 over by the end of the month.

The executive director of the Port Authority, Christopher Ward, will present his assessment of updated deadlines and budgets for the Freedom Tower, the museum, the memorial plaza, and the cultural and transit centers on Thursday. Mr. Ward’s report is expected to show, finally, how far behind schedule and how far over budget the project is.