LOS BANOS — The San Luis National Wildlife Refuge Complex, where tule elk bugle across grassy uplands and migratory waterfowl splash in languid sloughs, has been run for years out of a strip mall 12 miles away.

There is no money to build a visitors center on the 44,000-acre complex that provides recreation for about 90,000 tourists, anglers, hunters and bird watchers each year. Nor is there money to hire a second full-time law enforcement officer for the complex’s three far-flung refuges in Merced and Stanislaus counties.

So Ranger Anthony Merrill patrols the largest freshwater wetland complex left in California with a dog named Scott.

A high-energy, 80-pound Belgian Malinois, Scott can be a formidable ally when Merrill is tracking down poachers, breaking up altercations, searching for marijuana patches and meth labs, or investigating burglar alarms at refuge warehouses. But the pair can cover only one refuge at a time, although drug crimes, fish and game violations, vandalism, dumping and medical emergencies occur throughout the complex.

The National Wildlife Refuge System, part of the U.S. Fish and Wildlife Service, was created a century ago to provide a haven for the most imperiled species. But the mosaic of 547 refuges covering nearly 100 million acres of swamps, islands, wetlands, deserts, grasslands and forests is itself jeopardized by budget constraints.

Distributed across all 50 states, the refuges are home to hundreds of types of birds, mammals, reptiles, amphibians and fish — many threatened or endangered. But refuge managers say cutbacks are undermining efforts to protect an array of sensitive species, including red wolves, sandhill cranes, pronghorn antelope, sea turtles and rare butterflies.

More than 225 jobs at refuges were cut between fiscal 2004 and 2006, leaving some refuges with no employees. Many refuges operate without full-time law enforcement. Some are losing battles against invasive plant species that choke out wildlife habitat. Education programs for schoolchildren and others are being curtailed or dropped at some refuges. At the 1.5 million-acre Desert National Wildlife Refuge, the largest in the lower 48 states, there is no money to fix a washed-out stretch of a 75-mile dirt road from Las Vegas across the Mojave Desert in Nevada. Some visitors insist on driving through the closed section and get stranded. “I just hope someone does not die before I have the opportunity to have it fixed,” manager Amy Sprunger said.

In North Carolina’s Pocosin Lakes National Wildlife Refuge, half of the 100 miles of roads have been closed. “We can’t pay for materials to fix the holes,” manager Howard Phillips said.

At Southwestern Arizona’s Cabeza Prieta National Wildlife Refuge, manager Roger Di Rosa said he does not have staff to adequately monitor endangered Sonoran pronghorn antelope. The wilderness the animals once had largely to themselves has become a busy corridor for smugglers and illegal immigrants. “It is affecting them,” Di Rosa said. “Watching them over time, we feel it is hampering efforts of recovery.”

Bill Reffalt, who was national chief of refuges in the early 1980s, said habitat degradation was a nationwide problem.

“Hundreds of millions of birds and other wildlife depend on refuges ... and if you reduce the capacity of refuges to take care of them, the animals have no place to go,” he said. “They can’t just go buy a plane ticket.”

Refuge funding, now about $380 million annually, has remained relatively flat since 2003, while salaries and other operating costs have risen. Anticipating that domestic security, hurricane relief and the wars in Iraq and Afghanistan will remain higher spending priorities, officials are preparing to trim 75 regional and headquarters office jobs and 248 more field jobs in the next couple of years. That means the field staff will have been cut by one-sixth since fiscal 2004.

“I told them (managers) we can no longer do more with less if we are going to have quality delivery,” U.S. Fish and Wildlife Service Director H. Dale Hall said in a telephone interview. “We are going to have to do less with less and make ... intelligent management decisions. ... We are going to come out of this with a strong wildlife system.”

But many refuge managers aren’t so sure. Nearly two-thirds of them, responding to a recent survey by the nonprofit Public Employees for Environmental Responsibility, said the refuge system is not accomplishing its missions.

“I’ve been with this agency 30 years and have seen ups and downs, but I have never seen anything like this,” said Patricia Martinkovic, manager of the Minnesota Valley refuge near Minneapolis.

After losing 20 percent of her staff, Martinkovic said, the refuge is drastically reducing the mowing of 35 miles of trails, prescribed burning for fire protection and invasive plant control.

“Fast forward it a few years and you will see that wetlands have basically filled in with (invasive plants) and will not see that nice vista of egrets and trumpeter swans,” Martinkovic said.