Brown said the president is trying to gut the Endangered Species Act before he leaves office next month.
"Unfortunately, the Bush administration has had an antipathy to using sound science," Brown said in a phone interview with The Associated Press. "This is the latest assault as Bush goes out the door. It's intolerable."
The lawsuit was filed late Monday in U.S. District Court in San Francisco.
The Interior Department issued the revised rules this month. They allow federal agencies to issue permits for mining, logging and similar activities without getting a review from federal wildlife biologists if their own research shows the project will not affect plants and animals.
The changes also block agencies from using the Endangered Species Act to consider the effects of greenhouse gas emissions on ecosystems when reviewing projects such as new roads or coal plants on federal land.
Interior Department spokeswoman Tina Kreisher said the revised rules will continue to protect threatened and endangered species and noted that the law says federal agencies will ensure no listed animals are killed.
The lawsuit also names the U.S. Fish and Wildlife Service, the U.S. Department of Commerce and the National Marine Fisheries Service as defendants.
Brown is asking the court to block the new rules, which could give the incoming administration of President-elect Barack Obama time to review them.
Obama has said he would work to reverse the changes. Because they take effect before he is sworn in, Obama would have to restart a lengthy rule-making process that could last up to a year.
Three environmental groups also have filed lawsuits challenging the revisions, which they say erode protections for endangered species.
Current rules require biologists in the Fish and Wildlife Service and National Marine Fisheries Service to sign off on dams, power plants, timber sales and other projects even when it is determined they are not likely to harm species.
The revised rules will reduce the independent reviews that government scientists have performed for 35 years. The idea is to accelerate a process that developers and other federal agencies have blamed for delays and cost increases.
Between 1998 and 2002, the Fish and Wildlife Service conducted 300,000 consultations for projects proposed for federal land. The National Marine Fisheries Service, which evaluates projects affecting marine species, conducts about 1,300 reviews each year.
California's lawsuit alleges that the Department of Interior failed to adequately consider public comments critical of the revisions before it finalized the rules.
California is home to 310 plant and animal species listed as endangered or threatened by the federal government, more than any state except Hawaii, according to the complaint.