By Naoki Schwartz on MotherNatureNetwork.com

Gazing past the rolling whitecaps in the middle of San Diego's whale-watching season, boat captain Bill Reese was dismayed by what he wasn't seeing.

"Where are the whales?" said Reese. "Where are the whales?"

Long held as an environmental success story after being taken off the endangered list in 1994, California gray whales draw legions of fans into boats or atop cliffs to watch the leviathans lumber down the coast to spawning grounds in Baja.

But whale-watching skippers became alarmed after sightings dropped from 25 a day in good years to five a day this season. Such anecdotal evidence has left conservationists and state officials worried about the whale's future, especially now.

The federal government's monitoring of the mammals has fallen off in recent years. And the International Whaling Commission in June will consider allowing 1,400 gray whales to be hunted over the next decade.

The decision will rely on a report that says the population is flourishing — a study critics say is spotty and outdated.

"If you count 2,500 animals, all you really know rock solid for sure is there are more than 2,500. Beyond that you're using models and assumptions," said Stanford University marine biology professor Steve Palumbi. "The problem comes when you say, 'We do know how many whales there are and we're going to start making unalterable management decisions on that basis.'"

Number of calves has plunged

The study draws on annual population estimates dating from 1967, but in the past decade, only three census counts have been released, the most recent in 2006.

Since than, the estimated number of calves has plunged from more than 1,000 in 2006 to 312 in 2009. In addition, the species suffered a die-off of several thousand whales in 2000.

"You can't set specific quotas for 10 years based on 2006 data," said Sara Wan, a California Gray Whale Coalition member who is also a state coastal commissioner. "It's irresponsible."

In January, the California Coastal Commission pressed the National Oceanic and Atmospheric Administration for an updated gray whale study. The count is done but the analysis won't be finished until long after the whaling commission's decision.

NOAA scientists say their population estimates are reliable because the numbers have remained relatively consistent over time. They say the drop in calf numbers may reflect nature thinning out the herd.

The population is still more than double what it was in the 1960s and has been fairly stable of the past couple decades, said Paul Wade, one of the study's co-authors and a member of the commission's scientific committee.

"If it truly does go into an important decline, it's not going to happen overnight. We're going to see it," he said.

The gray whale's success has created a complex dynamic for NOAA researchers, who recently have focused on more threatened, less charismatic whales like the North Atlantic Right whales, whose population may be as low as 30.

Over the years, scientists have been able to do a great amount of research on gray whales because they are so accessible and popular with the public. Any indication of trouble galvanizes countless fans.

"Gray whales are our pets, they're in our backyard," said David Rugh, a NOAA biologist who oversaw gray whale counts for years. "Of course we have a concern about them going through so many environments from Mexico to the Arctic but there are other species out there that we're also concerned about."

Long migration

Gray whales migrate thousands of miles each fall from Alaska to Baja, then back north between February and May. They spend summers in the Bering Sea and Arctic.

Biologists sit in a little stand on California's central coast, counting adult whales as they swim south. Calves are counted as the whales make the return trip north. The counts are used to extrapolate overall population and monitor reproduction.

When gray whales were listed as endangered in 1970, an estimated 12,000 remained. A moratorium on commercial hunting and close monitoring helped the population rebound to more than 20,000.

Deemed recovered, the whales needed to be monitored only every five years, instead of annually, and there was no longer dedicated funding for the whales, which cost about $170,000 a season to count.

The 2006 count yielded about 2,500 whales, leading researchers to calculate about 20,000 whales total. The most recent calf count of 2009, however, revealed the fewest since 2001.

"These are troubling numbers," said Randy Reeves, chair of the Cetacean specialist group of the International Union for the Conservation of Nature. "If they're being reinforced by comments from whale watching guys, then it gets that much more troubling."

Wayne Perryman, who oversees NOAA gray whale counts, said he believes there is a correlation between lower reproduction rates and colder winters when lingering ice blocks whales from getting to feeding grounds. He also does not see reason to panic.

"I think it's like in a room when someone yells 'fire!'" Perryman said.

The whaling commission allows the Russian Chukotka people and the Makah Indian tribe in Washington to hunt 140 gray whales per year. While they typically revisit the issue every five years, the panel is considering limits through 2020.

Douglas DeMaster, the U.S. delegation's deputy commissioner, said the number is about half of one percent of the current estimated population.

"This is a very conservative number and provides subsistence needs to aboriginals," he said.

But Liz Alter, a marine biologist with the Natural Resources Defense Council, said, "Given that we have very little ability to predict what climate change, ocean acidification and other threats will mean to the whale population for the coming years, it seems reckless to me to set catch limits for that length of time."