HOBOKEN, N.J. — The fenced-off piles of rubble at the northern end of this city bear no resemblance to the limestone towers of Rockefeller Center in Manhattan. But the connection between the two plots on opposite sides of the Hudson River is at the core of Gov. Chris Christie’s latest political headache.

Hoboken’s mayor, Dawn Zimmer, has repeatedly and very publicly alleged that members of Mr. Christie’s cabinet applied pressure to get her to support a large-scale commercial development on the derelict lots in her city. Those lots are owned by the Rockefeller Group, which built Rockefeller Center and is represented by the law firm of a close associate of Mr. Christie.

Ms. Zimmer, a Democrat, said that Lt. Gov. Kim Guadagno told her that federal money for rebuilding and fortifying Hoboken against another storm like Hurricane Sandy would hinge on her backing of the project. The mayor said Ms. Guadagno, a Republican, told her that Mr. Christie had sent her to deliver that message personally because the project was so important to him.

Those allegations came just days after Mr. Christie, whose second inauguration is Tuesday, apologized for the intentional disruption of traffic in nearby Fort Lee in a retribution scheme engineered by some of his associates. But the Christie administration is not conceding Ms. Zimmer’s charges. On Monday, Ms. Guadagno disputed Ms. Zimmer’s account of their meeting at a Shop-Rite supermarket in May.