Mohammed Nuru has resigned his post as director of San Francisco Public Works, some two weeks after his arrest on fraud charges pitched the city into a widening government corruption scandal.

The resignation preceded an expected dismissal.

Nuru had been on paid administrative leave since he was arrested along with San Francisco restaurateur Nick Bovis on Jan. 28.

City Administrator Naomi Kelly, Nuru’s supervisor, accepted his resignation Monday morning.

Multiple people with knowledge of the matter confirmed that Nuru was cooperative with the city attorney’s office’s investigation that launched following Nuru’s arrest two weeks ago.

Soon after Nuru was arrested, the public and some local officials asked why he couldn’t be immediately fired. But California law prohibits employers from firing anyone only because they’ve been arrested.

“While I understand the desire for him to be fired immediately, it’s important that we follow all the laws required to terminate a public employee, no matter the circumstances. Before this process had been completed, he submitted his resignation,” Mayor London Breed said in a statement. “I will continue to support the full independent investigation underway to uncover any improper actions that were taken and recommend reforms to ensure they never happen again.”

Nuru will no longer collect his $273,000 annual salary, but the fate of his roughly $91,000-a-year pension isn’t yet clear. City law requires that an employee of the city and county of San Francisco be convicted of a crime of moral turpitude before the person’s pension can be taken away, and Nuru’s court case has only barely begun.

In a brief email to Kelly sent over the weekend, Nuru requested paperwork to apply for his full pension.

Nuru’s resignation marks the end of his decades-long career in and around San Francisco city government, but multiple investigations — by the FBI and a far-reaching internal probe by the city attorney and controller’s offices — continue.

In the wake of the charges, a coalition of city supervisors, led by Matt Haney, has called for yet another probe conducted by an outside firm untethered to city government.

Much of what’s known so far about Nuru’s and Bovis’ alleged schemes came to light when the Justice Department unveiled a 75-page criminal complaint meticulously documenting the findings of an investigation that used undercover officers, wiretaps and confidential sources. Many inside City Hall are wondering what’s yet to be uncovered.

On Friday, an official with San Francisco’s Department of Building Inspection confirmed reports that the agency had been visited by the FBI and was cooperating with the bureau’s investigation.

Breed appointed Alaric Degrafinried interim public works director to steer the department while she looks for a permanent replacement for Nuru. Degrafinried was the city purchaser, overseeing city contracts for most departments, not including Public Works.

Nuru and Bovis, the owner of the now-closed Lefty O’Doul’s restaurants, are accused of concocting several schemes, some of which were allegedly intended to steer city contracts to Bovis. Nuru has also been accused of accepting gifts from a billionaire Chinese developer in exchange for help with a development deal, lying to the FBI, and receiving free and discounted building materials that he did not disclose.

For years, Nuru ingratiated himself with powerful people, cultivating a reputation as the city’s go-to cleanup man and an indefatigable problem-solver for his allies. In years past, when city investigations into his behavior arose, Nuru could count on friends in high places — including mayors and supervisors — to come to his aid.

“Mr. Nuru is proud to have worked with so many committed and dedicated people over the years at Public Works,” said Ismail Ramsey, Nuru’s attorney. “He was part of a decades-long effort to help strengthen communities and empower city residents, especially disadvantaged youth and marginalized adults striving to rebuild their lives. Under his leadership, the revitalization of the city’s infrastructure and buildings ... has created an enduring impact.”

Haney said it was good that Nuru resigned.

“It shouldn’t have taken this long,” he added.

On Tuesday, Haney will announce his intent to put a charter amendment on the November ballot meant that would fundamentally restructure Public Works in an effort to increase transparency at the agency and boost its effectiveness.

San Francisco has become “infamous for being disgusting. The mess on our streets is connected to the mess in city government,” said Haney, who represents some of the most stubbornly filthy neighborhoods in the city, including the Tenderloin and South of Market.

Just over a year into his first term as supervisor, Haney has been a relentless critic of what he sees as Public Works’ inconsistent and ineffective approaches to street cleaning — issues rooted in the “huge” amount of power and responsibility conferred on the Public Works director, he said.

The charter amendment has been in the works for months, Haney added, long before the revelations of Nuru’s alleged self-dealing came to light.

Haney’s ballot measure would split Public Works in two, creating an entirely new city agency: the Department of Street Cleaning and Sanitation, which would focus on street and sidewalk cleaning, waste management, illegal dumping, and maintaining public toilets.

The state of the city’s streets “hurts quality of life; it hurts our economy, and it’s a public health crisis. Someone should be accountable for that,” Haney said.

The rest of Public Works would then handle roles like construction permitting and management, urban forestry and engineering work.

Both departments would also answer to their own oversight commission. The full scope of the commission’s responsibilities is still being determined, but Haney said it would provide more oversight of the department’s top brass.

“There’s been a massive breakdown in accountability,” Haney said.

Dominic Fracassa is a San Francisco Chronicle staff writer. Email: dfracassa@sfchronicle.com Twitter: @dominicfracassa