The leaders of two of the most powerful governmental institutions in San Francisco are at odds over how to deal with one of the city’s most enduring problems, demonstrating how little agreement there is when it comes to tackling homelessness.

Mayor Ed Lee has condemned San Francisco Superior Court’s recall of 64,713 outstanding arrest warrants for quality-of-life offenses dating back more than five years. Lee said he is “emotionally angry” about the decision and refuses to accept it.

Presiding Judge John Stewart says it is a waste of resources to keep track of warrants that are rarely enforced and fines that are almost never paid.

“No one is taking these warrants seriously and for good reason,” Stewart said, adding that Lee can’t do anything to reverse the court’s action.

The disagreement heightens an already rocky relationship between Lee and San Francisco judges. And it demonstrates the lack of coordination among city officials, the courts and law enforcement, each of which plays a critical role in dealing with the homelessness crisis.

On Oct. 18, Superior Court Judge Christopher Hite issued a court order suspending the fines and recalling the outstanding arrest warrants for quality-of-life citations, which can be given for everything from sitting on public sidewalks to urinating in public to building illegal encampments.

Court spokeswoman Ann Donlan said Hite’s order “was a collective decision by the court,” which saw it as being in line with the court’s decision in October 2015 to not issue warrants for people with unpaid traffic tickets.

Since then, Stewart said, he has tried to meet with the mayor to explain the decision, but was told that Lee didn’t have time to meet until January — when the court will have a new presiding judge. In the meantime, both sides are making their case publicly in largely moral terms.

Lee said this week that he “cannot have judges” who overlook citations simply because they may hurt poor people.

“What is the benefit of that except to put the entire burden and responsibility on the city to figure it out?” he asked. Lee also said the city needs to use “tougher love” to make people accept services and help.

He said that it’s clear that someone who, say, gets 10 citations for urinating on the same street has some kind of illness and that enforcing citations can be used to get that person into the city’s Community Justice Center. The center is overseen by the Superior Court and allows low-level crimes to be wiped from someone’s record if he or she accepts services, such as entering into a drug treatment program.

“My theory is you’re going to have multiple citations for certain individuals. They’re going to be the ones that you know are in very deep challenges with their health,” Lee said.

He added that he is working to expand the number of beds for the mentally ill at San Francisco General Hospital and that people who pile up stacks of quality-of-life citations may be good candidates for those beds. Citations should be used to compel them to accept treatment, the mayor said.

But Stewart said arresting people who failed to pay the citations penalized the poor and mentally ill instead of helping them. The problem, he said, is most people don’t appear in court — the judges and court staff estimate around 10 to 20 percent show up.

Before Hite’s order, the court issued a bench warrant for those people who didn’t pay or show up to court. The police could act on those warrants and take the person to jail.

“We are not going to put people in jail” for failing to pay a fine, Stewart said.

In fact, that rarely happened, said San Francisco Sheriff Vicki Hennessy. A report by the city’s budget and legislative analyst released in June found that just 2 percent of quality-of-life citations in 2015 resulted in arrest.

And unless a judge made a special note to detain the person, the sheriff’s deputies usually gave the individual another citation, released the person and told him or her to return to court in two weeks or a month, Hennessy said.

“You don’t want to have people in jail just because they couldn’t pay a fine.” Hennessy said. She said it’s becoming increasingly clear to her that getting people services “before they even get a citation, before they are criminalized in any way, shape or form, is where the investments need to be.”

Still, Hennessy said she was surprised by the court’s decision to recall the warrants. “It would have been nice to have a discussion — just so we are all on the same page.”

And while Hite’s order suspended the fines and fees for people who received quality-of-life citations between Jan. 1, 2011, and Oct. 30, 2015, anybody who received a citation after that date — or who receives one anytime in the future — still is fined around $200. If they fail to appear in court, the court tacks on a $300 late fee. If they never pay it, a collections agency could get involved to track down the debtor.

Interim Police Chief Toney Chaplin said arrests should remain an option.

“Writing the ticket is an incredibly time-consuming thing for the officers on the streets,” Chaplin said. “We don’t do it with the thought that it’s going to be a revolving door. We do it with the thought that at the end there is going to be some type of consequence or solution.”

San Francisco supervisors are also taking sides.

“Taking potshots at the judicial branch is a slippery slope,” said Supervisor Aaron Peskin, a frequent critic of the mayor. “It’s easy to point fingers at the court, but fundamentally why are we issuing citations to people who can’t pay them when we could be spending the same amount of financial resources on mental health care and housing the poorest of the poor.”

Supervisor Mark Farrell, a leader of the board’s moderate bloc, said he agrees with Lee.

“There has to be consequences to breaking the law, and if our courts are dismissing these warrants, individuals on our streets have little incentive to abide by the law and listen to our police officers,” he said.

This is not the first disagreement between Lee and San Francisco judges. In May, Lee blamed them for the rising rate of property crime.

He said judges ought to be “held accountable” if they don’t give tough enough sentences to people repeatedly charged with car break-ins and other property crimes. Stewart retorted that many low-level property crimes are committed by people with drug addiction and mental health problems who should be in special programs — not jail — and that it was not the moment for one branch of government to blame the other.

Stewart reiterated that sentiment this week.

“We are saying, let’s work together,” he said.

Emily Green is a San Francisco Chronicle staff writer. Email: egreen@sfchronicle.com

Twitter: @emilytgreen