The director of an embattled federal immigration agency will step down from his position, leaving the agency in limbo as it struggles to wade through a flood of citizenship applications before the presidential election.

Emilio Gonzalez, an immigrant from Cuba who was appointed by President Bush in 2005 to head the United States Citizenship and Immigration Services, told agency staff in an e-mail that he was resigning to spend more time with his family. Mr. Gonzalez’s agency faced a drumbeat of criticism in recent months from immigration lawyers, advocates, and immigrants who said it was unprepared for the surge in citizenship applications that came just before a 69% fee increase was implemented in July 2007.

At the urging of a major national campaign by Hispanic groups, hundreds of thousands of Hispanic immigrants had applied for
citizenship around the same time in anticipation of the upcoming presidential election. The groups, including the National Association of Latino Elected and Appointed Officials, said they warned USCIS officials about a likely increase in the number of applications as a result of the campaign.

Nevertheless, USCIS seemed to be caught unprepared when citizenship applications rose nearly 650% in one month in July compared to the previous year. The number of applications total last year was more than 1 million, the most in 10 years and double the number filed in 2006, according to numbers released by the USCIS in January.

The surge more than doubled wait times for immigrants hoping to become citizens, to as many as 18 months, threatening to keep many from voting in November.

The director of the Migration Policy Institute at New York University Law School, Muzaffar Chishti, called the increase in fees and the ensuing “deluge” of applications “both a policy and a management failure.”

“They might have predicted that this was going to lead in a big increase in the backlog,” Mr. Chishti said. “Clearly they did not.”

Immigration lawyers have also expressed frustration with the performance of the USCIS in recent years.

“He really barely rearranged the deck chairs on the Titanic, and has really not done anything to ameliorate the problems of the past few years,” the president of the Academy of Business Immigration Lawyers, Angelo Paparelli, said.

As recently as two weeks ago, however, in an interview with the New York Sun, Mr. Gonzalez had seemed upbeat about the agency’s progress in reducing the backlog.

“This is something we foresaw. We made some internal adjustments,” he said in an interview after presiding at a citizenship ceremony at Stuyvesant High School in Manhattan, adding: “I would be dishonest if I said we foresaw the scope.”

“We adjusted to it, we hired 3,000 people this year, we’re moving people around,” Mr. Gonzalez said. “In the aggregate, we’re actually going to naturalize more people this year than we did last year.”

Mr. Gonzalez had said the fee increase was needed in order to update technology at the USCIS and hire more staff. Part of the money is going to the FBI to streamline background checks for prospective citizens, where backlogs have kept some immigrants in limbo for years.

Now, the agency itself is in limbo after the second leader since its inception in 2003 has left. USCIS officials said they could not comment yesterday on who might replace Mr. Gonzalez, or whether he would be replaced at all with the Bush administration on its way out in less than a year.

Senator Kennedy, the Democrat of Massachusetts who is chairman of the immigration, refugees, and border security subcommittee of the Senate Judiciary Committee, responded to news of Mr. Gonzalez’s plans by issuing a statement that said, “The path to citizenship in our country is in crisis. As we approach the election, over a million people who are qualified and eager to become citizens are stuck in line. Many will be denied the right to cast their first ballots as American citizens this fall. The president must commit himself to fixing this intolerable situation and he should start by choosing a strong and committed leader to take over this office.”

The Washington D.C. director of the National Association of Latino Elected and Appointed Officials, William Ramos, said his organization would continue to pressure the new leadership to focus on reducing the backlog before the election this fall.

“We hope that moving forward that new leadership makes reduction of the immigration backlog a priority,” Mr. Ramos said. “I can tell you that this issue is not going to go to the backburner. We’re not going to let it.”

In his e-mail to staff, the only reason Mr. Gonzalez gave for his departure was his desire to spend more time with his wife and children, who live in Florida.

“I am very proud of the many accomplishments achieved by USCIS over the past two years,” Mr. Gonzalez wrote. “Those accomplishments are the result of the tireless energy and dedication of our 17,000 government employees and contractors. Together we have taken this agency to new heights.”

The Homeland Security Secretary, Michael Chertoff, praised Mr. Gonzalez’s performance as the USCIS director, saying he would “leave an indelible mark on the transformation and modernization of USCIS operations.”

Mr. Chishti said that aside from the backlog, Mr. Gonzalez had achieved several major accomplishments as USCIS chief. This year, he finally implemented a new citizenship test — in the works for about a decade — that is intended to be more meaningful than the previous test. He also made himself available to immigrant advocacy groups and other stakeholders in the immigration debate, Messrs. Ramos and Chishti said.

Before arriving at USCIS, Mr. Gonzalez served as a diplomat and a foreign policy adviser to President Bush. His last day at the agency will be April 18.