The FBI said it had a search warrant for several offices but declined to be more specific.
Recently appointed city business administrator Sam Hutchinson, whose department was among those being searched, told The Trentonian newspaper that FBI agents were also in the office of Mayor Tony Mack.
"The FBI is searching through documents in his office," he told the newspaper.
Mack, 46, on Wednesday denied wrongdoing after the FBI spent the overnight hours searching his home, and the homes of his brother, Ralphiel Mack, and businessman Joseph Giorgianni, a campaign donor who is a convicted sex offender. An email message left Thursday for the mayor's top aide was not immediately returned.
The Democrat's first two years in office have been marked by repeated accusations of reckless spending, cronyism and mismanagement.
Questions have also lingered about how Mack financed his 2010 campaign at a time of personal financial problems. His home and other properties have faced foreclosure, and last month the city reported that he, his brother and Giorgianni all were late making property tax payments.
Mack had a disastrous record of filling top jobs at City Hall, which led to an agreement last year with the state that allows him to hire department heads only from a state-approved pool of applicants or risk losing $6 million in state aid.
In his first year, one of a string of business administrators resigned just ahead of pleading guilty to embezzlement on another job. His housing director quit after it was learned he had a theft conviction. His chief of staff was arrested trying to buy heroin.
His half brother, Stanley "Muscles" David, pleaded guilty earlier this year to official misconduct for directing Trenton Water Works crews to perform private side jobs using city equipment and billing the city.
Mack is also the target of several wrongful-termination lawsuits. One former employee in the recreation department complained she was laid off in part because she had inquired about missing city funds.
The Times of Trenton newspaper said one of its reporters saw FBI agents in the recreation department offices on the third floor.