Early one morning in 2007, Muhammad Chaudhry showed up at the Islamic Center of East Bay in Antioch, Calif., and found seven bullet holes in one of the building's front windows.
Soon, agents from the San Francisco office of the Federal Bureau of Investigation arrived and documented it and previous incidents at the center. In 2005, someone had left messages including "racial slurs" on the center's answering machine, the agents wrote. In 2006, a single shot had damaged a window; a few months later, the same window was destroyed with a brick.
In a report written three weeks after the shots were fired, and obtained through a Freedom of Information Act request, an agent wrote that no investigation would continue "since there is no current evidence to show this incident as being a hate crime."
Six months later, arson gutted the center. F.B.I. agents opened an investigation, but members of the center wondered whether the fire could have been prevented if the agency had pursued the fusillade that preceded it.
All of the episodes at the center "were consistent in targeting us," and an investigation into the shooting "would have been helpful," Abdul Rahman, the chairman of the center's board of trustees, said recently. "Now we'll never know if these involved the same people."
The F.B.I. did not respond to specific questions about the things that happened at the center and another case from the same year, because some of the agents that worked in the San Francisco office in 2007 have since left, said Julianne Sohn, a bureau spokeswoman there.
She added that it was also hard to comment on individual reports without knowing if there were other related documents, but said that the F.B.I. was dedicated to looking into any hate crimes that were reported.
"Here in the Bay Area, we take hate crimes very seriously," Ms. Sohn said. "Whenever we get any kind of allegation or complaint we look at it thoroughly."
Reservations over how the situation at the center in Antioch was handled underscore a sometimes delicate relationship between the F.B.I. and the Muslim population near San Francisco.
About a year ago, a Freedom of Information Act request by the American Civil Liberties Union of Northern California and other groups yielded about 15,000 documents detailing interactions between FBI agents and Muslims in that part of the state.
Lawyers and activists said that the documents showed that the F.B.I. had used a mosque outreach program, meant to combat hate crimes directed at Muslims, to gather information about people engaged in lawful activities. News reports followed, along with debates over how the F.B.I. should approach the Muslim population. At the time, F.B.I. officials said those operations were appropriate.
But most of the thousands of pages the F.B.I. turned over received little or no attention. Among them were reports that documented a handful of instances in which agents declined to pursue possible hate crimes.
Although the F.B.I. requires that agents examine all such claims, not all result in a full investigation. Some lack dependable evidence, and agents may determine that others do not include hate-crime components as defined by federal law. Ms. Sohn said that it could be hard to find proof of intent, a key element in demonstrating that a hate crime took place.
But Michael German, a former F.B.I. agent and now a senior policy counsel for the A.C.L.U. in Washington, said that two instances in which the San Francisco office did not pursue investigations stood out.
One involved a graduate student at the University of California, Berkeley, who told agents in 2007 that he had received threatening calls from blocked numbers after including his phone number on fliers promoting an antiwar protest.
One caller told the student to be "very, very careful," an F.B.I. report stated and added, "You wouldn't want an accident to happen to you."
The second used a racial epithet, the agents wrote, and told the caller to blow himself up "before we do it for you."
The report went on to note that F.B.I. records indicated that a person whose name was redacted, apparently the student, had previously written e-mails that "conveyed hatred toward the United States and Israel and support for the Palestinian cause."
A man named Snehal Shingavi said he was the one who had received the threats and spoken with the F.B.I. He said that the agency had not accurately characterized the views he had expressed in e-mails and added that it was improper to catalog political opinions attributed to him.
"The linking of my political activity with the decision not to fully investigate the death threats is very troubling," Mr. Shingavi said.
Also troubling, Mr. German said, was the decision not to start a hate-crime investigation after shots were fired at the Islamic Center of East Bay, given the escalating nature of the attacks there. An investigation, he said, could have solved or deterred crimes and helped foster trust between the F.B.I. and the center.
"Here was an opportunity to do something to protect the community," Mr. German said. "There is concern in the community that the F.B.I. is viewing them through only one lens, as potential suspects."
Mr. Rahman, from the center in Antioch, said that agents began contacting him regularly after the arson there, sometimes taking him to lunch. He was eager to establish a rapport, he said, but became uncomfortable when questions about the fire seemed to give way to questions about the center's members.
"After you've been victimized, that is not something you want to hear," Mr. Rahman said, adding that he cautioned the agents that their work in general would not benefit from such an approach, telling them: "You're not going to build a relationship this way."
This article originally appeared in The New York Times.