NEW YORK (CNN) - The owner of the World Trade Center site and the real estate developer who leased it six weeks before a terrorist attack destroyed the complex have reached a new agreement that will finance the building of new office towers and juggle who ultimately controls them.

The Port Authority of New York and New Jersey, the transportation agency that built the 110-story twin towers in the early 1970s and ran them until July 2001, approved the deal with developer Larry Silverstein in a board meeting Wednesday afternoon.

"We agreed to all of the port's economic terms in its proposal to restructure our 99-year lease," Silverstein said. "This is a fair deal."

It is the third time since the Sept. 11, 2001, terrorist attacks destroyed 12 million square feet of office space that Silverstein's firm has amended his $120 million-a-year lease. He has never stopped paying rent, though he has not collected any revenue since the attacks.

Under the deal's terms, Silverstein will cede control of the iconic Freedom Tower, the planned 1,776-foot building to rise on the northern half of the 16-acre site, to the Port Authority. Silverstein will collect a 1 percent developer's fee on the estimated $2 billion project, but the Port Authority will manage the building when it is completed in 2010.

A memorial to the 2,973 Sept. 11 victims and six people killed in a 1993 truck bombing will be centered in the southern half of the site. It is expected to be completed in 2009, financed through private donations.

Under the deal, Silverstein will retain control of three buildings planned along the site's eastern edge, Church Street, which will house much of the street-level retail space. He will receive a 2 percent developer's fee for those buildings, due to be completed in 2012. One is a 950-foot tower to be designed by renowned British architect Norman Foster.

Silverstein will cede control to the Port Authority of a plot of land across the street from the site's southern end, where a fifth building would go, according to the master plan. The damaged Deutsche Bank building that stands there is being dismantled, possibly for a new residential tower.

Overall, the five planned buildings will create 10 million square feet - approximately 6.2 million square feet for the three Church Street buildings, 2.6 million square feet in the Freedom Tower, and as much as 1.2 million square feet in the fifth building.

The Port Authority will significantly reduce Silverstein's rent, though the figures were not disclosed.

Silverstein will allocate to the Port Authority 38 percent of the $3.34 billion in tax-exempt Liberty Bonds he is due to received from the state and the city and a portion of approximately $3 billion in insurance proceeds he is due to collect.

"We have made real concessions," Silverstein said. "This is about moving the rebuilding forward as quickly as possible. All the finger-pointing must stop, and we must all work together to achieve our vital mission - to fully revitalize and renew New York's historic downtown region."

Silverstein, who lost four employees in the Sept. 11 attacks, said rebuilding is "an intensely personal endeavor for me."

He has already built, one block north of the site, an office tower that replaced World Trade Center 7, which he developed in the 1980s before taking over the whole site. A quarter of the building, 10 of the 42 habitable floors, are now leased. Next month, Silverstein Properties will be the first tenant to move in.

In recent weeks government officials had begun to question whether Silverstein's financial position was strong enough to continue as the designated WTC site developer, leading to the protracted negotiations.

Gov. George Pataki said the new plan "ensures that construction on the Freedom Tower will move forward in upcoming weeks and expedites the rebuilding of the entire WTC site." The governor said the rebuilt trade center will "anchor the financial capital of the world and make our nation proud."

Freedom Tower construction will move forward next month with installment of foundation footings. The tower itself will rise 1,360 feet, the height of the original twin towers, and a spire on top that will take the height to a symbolic 1,776 feet.

------------------------------------

Developer accepts new World Trade Center plan.