UPDATE 2-NY-NJ agency, World Trade Center developer in deal

(Adds comment from Silverstein, background)

NEW YORK, March 25 (Reuters) - The Port Authority of New York and New Jersey on Thursday reached a framework agreement with the developer of the World Trade Center, ending a 16-month stalemate over rebuilding at the site destroyed in the Sept. 11 2001 attacks.

Port Authority Executive Director Chris Ward said the agreement will clear the way for the developer, Larry Silverstein, to resume the building of his planned towers at the Ground Zero site in downtown Manhattan, subject to certain conditions.

The reconstruction effort has suffered long delays as the Port Authority and Silverstein have fought about money, security, designs and funding, frustrating officials, residents and families of the almost 3,000 people killed in the attacks that felled the twin towers.

Silverstein, under an agreement struck in 2001 and amended in 2006, is responsible for building World Trade Center Towers 2, 3 and 4, while the Port Authority is responsible for developing One World Trade Center and Tower 5, along with the WTC Transportation hub, the 9/11 Memorial, underground parking and retail outlets.

Building of One World Trade Center is under way, but Silverstein's projects have been held up in funding disputes.

Thursday's agreement creates a framework under which the reconstruction effort will be paid for using private funds, Liberty Bonds and money from New York state and city.

The Liberty Bond program was set up to create tax-free financing for reconstruction and to support the downtown Manhattan economy after the attacks.

The deal will allow for the east side of the site to be restored to street level, for Tower 4 to be completed by 2013 and for the phase-in of Towers 2 and 3 over time, the agency said in a statement.

Silverstein can immediately resume building the Tower 3 transit and retail podium, as long as he raises $300 million of private equity, preleases 400,000 square feet and obtains private financing for remaining costs.

Silverstein will receive a capped public backstop of $390 million from the agency, New York state and city to help him raise financing, as well as $210 million of equity from the state and city.

Silverstein, who had leased the World Trade Center complex just two months before the attack, welcomed the agreement and said it will accelerate the rebuilding and help revive the downtown economy.

The rebuilding effort has also been hurt by the real estate slump and recession, which hurt demand for office space and made banks reluctant to make risky loans.

Silverstein had lobbied hard for the Port Authority to guarantee his loans, but the agency was reluctant to use funds needed for public transportation links to a private party.

A number of New York officials have intervened to end the impasse, including New York Governor David Paterson, New York City Mayor Michael Bloomberg, Assembly Speaker Sheldon Silver and New Jersey Governor Chris Christie. (Reporting by Ciara Linnane; Editing by Leslie Adler)