There were 27 wolves in Arizona and 15 in New Mexico.
"I'm extremely disappointed and troubled about this year's low numbers," Fish and Wildlife Service regional director Benjamin Tuggle said Friday. "These findings are very disturbing and I am determined to identify the reasons for this decline and turn the situation around."
The survey classified two pairs of wolves as breeding pairs, the same number counted in 2008.
The reintroduction program in the Blue Range, straddling both Southwestern states, began with 13 wolves in 1998. Biologists had predicted a self-sustaining wild population of 100 wolves by now. Federal officials say the number has fluctuated because of deaths, births and removals.
The leader of a conservation group said the results raise "grave concerns" but expressed hope the situation could improve if federal officials introduce new wolves to replace those that have died and broaden the genetic lines of wolves roaming the 4-million-acre recovery territory.
Michael Robinson of the Center for Biological Diversity also proposed adding three new wolves anytime one is found dead, whether by poaching or natural causes.
"I don't want to sugarcoat it. The Mexican wolf is facing a genetic and demographic emergency," Robinson said. "Nonetheless, with science-based action, we believe the species can be salvaged."
Federal officials cautioned that several documented wolves couldn't be located during last month's count. Fish and Wildlife spokesman Tom Buckley said only wolves wearing radio collars can be accurately tracked, along with any wolves without collars accompanying them.
"To say there were many uncounted wolves might be pushing it a little bit, but we believe there are others that were uncounted," Buckley said.