The site was targeted Friday by the group, which replaced the content with an anti-police hip-hop music video and a message saying the action was in retaliation for the eviction of Occupy Boston protesters from Dewey Square, the Boston Herald reported.
BPDNews.com was partially restored to some users Wednesday, but officials said restoring the site to all visitors could take some time.
"We are making progress, but I am hesitant to give a specific time frame at this point," Boston police spokeswoman Elaine Driscoll said.
Meanwhile, the FBI said an investigation into Anonymous has been ongoing for more than a year.
"With this issue and these individuals, we don't put our names out there," an FBI spokesperson said. "Their attacks are not sophisticated, but they are nevertheless criminal."
The FBI's Web site was taken down by the group for a few hours last month after federal authorities shut down a file-sharing Web site and arrested the operators.