The agency responsible for overseeing more than $20 billion of construction in Lower Manhattan is in danger of being disbanded because financing from the state, the Metropolitan Transportation Authority, and the Port Authority of New York and New Jersey has not been forthcoming, according to several sources.

The hybrid city and state agency known as the Lower Manhattan Construction Command Center is in charge of coordinating the development of the World Trade Center site, including plans for a new PATH Station, the MTA’s Fulton Transit Center, and the construction of developer Bruce Ratner’s 75-story Beekman Tower, among others.

The agency is facing a budget shortfall of about $9 million, according to officials from the Lower Manhattan Development Corp., which controls the Command Center. The Port Authority owes about $5.2 million and the MTA owes $3.8 million. Both entities are controlled by Governor Paterson.

A board member of the LMDC, Edward Molloy, said the issue of withheld funds has been raised repeatedly at recent board meetings. Mr. Molloy said if the funding problem is not resolved the Command Center could “more or less disappear.”

“It doesn’t make much sense to stop financing LMCCC when we need a vehicle to make all construction get started and then coordinate it,” he said.

Established by Governor Pataki and Mayor Bloomberg in 2004, the Command Center relies on the LMDC for its financing needs, but counts on a number of stakeholders, including the state, the Port Authority, the MTA, the city, the transportation department, and the Federal Transit Administration to contribute to its operating budget.

The city has paid its share, and now city officials are calling on the state-controlled entities to pay up.

“Because the Command Center is essential to the quality of life for Lower Manhattan, residents living in the midst of more than $20 billion in construction projects, we remain committed to funding it and hope that our partners at the state will also meet their commitments,” a spokesman for Mayor Bloomberg, John Gallagher, said in a statement.

The president of the LMDC, Avi Schick, who is responsible for delivering the funds to the Command Center, said in an interview yesterday that talk of disbanding the Command Center is an exaggeration. Mr. Schick said he is confident that any outstanding balance owed by the Port Authority and the MTA would arrive by the next board meeting, scheduled for the middle of June.

“I am confident that they will pay what they owe,” he said.

Mr. Schick said he is seeking “a more formal agreement” for the Command Center’s financing, but he defended the state’s commitment.

“Are there technical issues? Absolutely. But is there a commitment on the part of the state? Of course,” he said.

A search committee is said to be closing in on a replacement for Mr. Schick, an appointee of Governor Spitzer who has said he will be returning to the private sector in the fall.

Still, Lower Manhattan residents are worried that a lack of construction oversight would create traffic and pollution problems and possibly lead to deteriorating safety conditions.

“This is really disconcerting,” the president of Lower Manhattan’s Community Board 1, Julie Menin, an LMDC board member, said yesterday. “We are about to the head into the peak of the construction year and it is imperative that the LMCCC has the funding that it needs so businesses and residents aren’t overly impacted. We are absolutely concerned about this.”

A spokesman for the MTA, Jeremy Soffin, said the MTA is “committed to providing our share of the funding.”

A spokeswoman for the Port Authority, Candace McAdams, said the agency is working with the LMDC on an agreement.

A spokeswoman for the Command Center declined comment.