The World Trade Center site’s owner turned over land where two office towers are planned to developer Larry Silverstein, clearing the way for construction to begin soon on more skyscrapers at ground zero.

The Port Authority of New York and New Jersey finished excavating the land for the towers on Sunday, 48 days behind a deadline it set for itself in an agreement with Mr. Silverstein. The agency paid $14.4 million in late fees to the developer. It said it partially made up for the cost by not paying the contractor a $10 million bonus it would have received for finishing on time.

The Port Authority worked for more than a year to build 80-foot-deep foundations for two towers that Mr. Silverstein will build, removing nearly 400,000 tons of concrete, soil and rock. Mr. Silverstein had said that construction would begin on the towers within weeks after the land was turned over.

Mr. Silverstein held the lease to the trade center complex when it was destroyed on September 11, 2001. The Port Authority renegotiated his lease in 2006, taking over the building of two of five planned office towers.

The agency agreed to excavate the eastern half of the lower Manhattan site for Mr. Silverstein’s towers by set deadlines or pay $300,000 in fines a day. It has until June to excavate space for a third tower.

The skyscrapers, all at least as tall as the Empire State Building, are expected to be built in the next four years. Construction is under way at the site on a 1,776-foot building called the Freedom Tower, a September 11 memorial, and a transit hub.