Nicholas B. Dirks, chancellor of the University of California at Berkeley, is stepping down from the post amid a string of controversies, ranging from budget troubles to the way the flagship university has handled sexual harassment allegations involving the faculty.

He also faced questions raised in a Los Angeles Times report in July about alleged misuse of public funds for travel and the personal use of a campus fitness trainer.

“Over the summer I have come to the personal decision that the time is right for me to step aside and allow someone else to take up the financial and institutional challenges ahead of us,” Dirks said in a statement to the campus community. Dirks, Berkeley’s 10th chancellor, has been in office since June 2013. He said his resignation will become effective when a successor is in place.

The president of the UC system, Janet Napolitano, said Tuesday that she had accepted Dirks’s resignation.

“I do so with deep appreciation for Chancellor Dirks’s efforts on behalf of this great institution, its students, faculty, staff, alumni and the larger Berkeley community,” Napolitano said. “We will immediately form a committee to begin a global search for the new chancellor, and Chancellor Dirks intends to stay on until a new successor is named and in place. We seek nothing less than an individual of the highest caliber to lead Berkeley, widely and correctly regarded as the finest public research university in the world. UC Berkeley, and the University of California, deserve nothing less.”

For the UC system, which has 10 campuses, the abrupt announcement from Dirks marks the second leadership shake-up in recent days. The chancellor of UC Davis, Linda Katehi, resigned this month amid upheaval over numerous leadership issues, including her handling of the aftermath of a 2011 incident in which campus police used pepper spray against student protesters.

Berkeley, with a star-studded faculty, is perennially ranked as the nation’s top public research university and has a premier global reputation. But in April, Dirks disclosed that the university would be cutting 500 staff positions over two years in an effort to erase a large budget deficit. The cuts amounted to a 6 percent non-faculty workforce reduction, seen as a surprising fiscal setback for a school with such a sterling brand.

In addition, Berkeley has been rocked by charges that the administration is too lenient in disciplining faculty members who face sexual harassment allegations. The Associated Press reported that Sujit Choudhry, a former dean of the law school, received a temporary pay cut and orders to undergo counseling as punishment after an investigation substantiated claims that he repeatedly kissed and touched a subordinate.

Dirks, a historian and anthropologist who is an expert on South Asia, came to Berkeley after serving as an executive vice president at Columbia University. He plans to remain on the faculty after leaving the chancellorship. He came to office pledging to improve undergraduate education at Berkeley and has sought to champion the role of public research universities at a time when many of them are under fiscal strain. Berkeley, like many other prominent universities, in recent years has stepped up enrollment of out-of-state students, who pay higher tuition, to help improve its finances.