The tiny St. Nicholas Greek Orthodox Church is once again at the forefront of the myriad disputes that plague the rebuilding effort at ground zero.

The fate of the church, a narrow whitewashed building that was crushed in the attack on the World Trade Center, was supposed to have been settled eight months ago, with a tentative agreement in which the church would swap its land for a grander church building on a larger parcel nearby, with a $20 million subsidy from the Port Authority of New York and New Jersey. This would have allowed work to begin at the south end of the site.

But the two sides never came to final terms. After months of negotiations, the Port Authority, which is overseeing reconstruction at ground zero, ended its talks with the church on Monday, saying that the church had sought increasingly costly concessions.

Complaints, of course, abound on both sides.

The authority now says that St. Nicholas is free to rebuild the church on its own parcel at 155 Cedar Street, just east of West Street. The authority will, in turn, use eminent domain to get control of the land beneath that parcel so it can move ahead with building foundation walls and a bomb-screening center for trucks, buses and cars entering the area.

“We made an extraordinarily generous offer to resolve this issue and spent eight months trying to finalize that offer, and the church wanted even more on top of that,” said Stephen Sigmund, a spokesman for the Port Authority. “They have now given us no choice but to move on to ensure the site is not delayed. The church continues to have the right to rebuild at their original site, and we will pay fair market value for the underground space beneath that building.”

Last July, the Port Authority and the Greek Orthodox Church announced a tentative plan to rebuild the church just east of its original site, at Liberty and Greenwich Streets. The authority agreed to provide the church with land for a 24,000-square-foot house of worship, far larger than the original, and $20 million. Since the church would be built in a park over the bomb-screening center, the authority also agreed to pay up to $40 million for a blast-proof platform and foundation.

In recent negotiations, the authority cut the size of the church slightly and told church officials that its dome could not rise higher than the trade center memorial. The church, in turn, wanted the right to review plans for both the garage with the bomb-screening center and the park, something the authority was unwilling to provide. More important, authority officials said, the church wanted the $20 million up front, rather than in stages. Officials said they feared that the church, which has raised about $2 million for its new building, would come back to the authority for more.

The termination of negotiations is a major setback for the little church, a parish of 70 families that is nearly 90 years old. St. Nicholas officials had hoped to build an impressive structure, with a traditional Greek Orthodox dome, and a nondenominational center for visitors to ground zero. That will not be possible on the church’s original 1,200-square-foot lot, although church officials say they hope for reconciliation.

“We consider the rebuilding of the St. Nicholas Church a sacred obligation to the victims of 9/11, to the city of New York, to the people of America and in fact to the international community,” said Stavros H. Papagermanos, a spokesman for the Greek Orthodox Archdiocese of America. “We will continue to discuss in good faith and we believe that all parties involved are well-intended, and ultimately we will overcome any obstacles that have arisen.”

One person who was involved in the negotiations on behalf of the church, and who insisted on anonymity so as not to inflame the situation, criticized the Port Authority, saying it had made constantly shifting demands on St. Nicholas. Still, he said, the remaining issues were relatively small.

But it does not appear that the Port Authority is posturing. And while the Bloomberg administration expressed regrets about the impasse, officials said it was far more important to proceed apace with building a memorial, a transit center and other projects at ground zero.

St. Nicholas, a four-story church, became a symbol of resilience after it was destroyed, with George E. Pataki, then the governor, and Archbishop Demetrios, primate of the Greek Orthodox Church in America, vowing that it would rise again.

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