Just as a major corporation is negotiating to move 1,500 jobs out of Lower Manhattan, the city’s economic tsar says he is resigning.

The president of the Economic Development Corporation, Andrew Alper, is leaving his position on June 2, the mayor’s office said yesterday. A former top executive at Goldman Sachs, Mr. Alper has helped lead the city’s efforts to spur development in Lower Manhattan following the terrorist attacks of September 11, 2001.

Mr. Alper’s departure comes as the city is trying to stop Citigroup Incorporated from taking 1,500 downtown employees across the river to Jersey City. The bank is selling its 11-story building at 250 West St. and is reportedly negotiating to sublease space from the Union Bank of Switzerland in a 32-story tower in Jersey City.

Citigroup’s chief executive, Charles Prince, is co-chairman of the Partnership for New York City, a group charged with drawing businesses to the city.The possible move to New Jersey is drawing criticism from some elected officials, who say it would be a setback to economic rebuilding efforts downtown. “It’s certainly troubling that someone so highly involved in the Partnership would be considering this kind of move,” a congressman whose district includes Lower Manhattan, Rep. Jerrold Nadler, said. “We expect business leaders to be partners in the effort, and to hold up their end of the bargain.”

The speaker of the state Assembly, Sheldon Silver, yesterday sent a letter to Mr. Prince expressing “grave concern” over the possible relocation. “Such a move would be devastating to the economy of the city of New York at a time when the struggle to rebuild from the events of September 11, 2001, continues,” Mr. Silver wrote.

The chairman of the City Council’s Lower Manhattan Redevelopment Committee, Alan Gerson, said the move would be “foolish.” The deal with UBS is not complete, and a spokeswoman for Citigroup, Shannon Bell, said yesterday the company is “still considering its options.” While the employees that would move serve a “mix” of functions, a large portion are support staff, she said.

The building on West Street is likely to be converted to condominiums, and the company is looking for a more modern space. “We are working closely with Citigroup to address their needs and help them find appropriate space in New York City to retain the jobs housed at 250 West St.,” a spokesman for EDC, Andrew Brent, said.

While the city is trying to save the 1,500 jobs, officials are quick to note that a move would not significantly diminish Citigroup’s presence in New York, where it is the city’s largest private sector employer, with 27,300 workers. That figures includes an additional 4,600 jobs since 2004, when Citigroup announced expansion plans.

The city has not chosen a replacement for Mr. Alper, and officials plan to “cast a wide net” in their search, a spokeswoman for the mayor, Jennifer Falk, said. Whoever is chosen will likely cost taxpayers a bit more than did Mr. Alper, who was one of a group of top city officials — including Mayor Bloomberg, the mayor’s sister, Marjorie Tiven, and Deputy Mayor Daniel Doctoroff – who take salaries of $1 a year.