Some activists called the decline "heartbreaking," but the Mexico head of the World Wildlife Fund said the reduction "is not alarming."
WWF Mexico director Jorge Rickards said the previous year's large numbers were "atypical" and the monarchs had returned to their average population levels of recent years.
The government commission for natural protected areas said the butterflies' population was "stable," even though they covered only 2.8 hectares (6.9 acres) this year. That was down from 6.05 hectares (14.95 acres) the previous year. Because the monarchs cluster so densely in pine and fir trees, it is easier to count them by area rather than by individuals.
"During the most recent wintering season the norm has been for the butterflies to cover an average of about three hectares," Rickards said.
"The last season, 2018-19, was very good, with 6.05 hectares of forest cover, but it was certainly atypical, thanks to the fact that the first generation of butterflies in the spring of 2018 encountered favorable weather conditions to reproduce," he said.
In contrast, butterflies in the spring of 2019 encountered colder weather in Texas than the previous year, and thus were less able to reproduce.
Millions of monarchs migrate from the United States and Canada each year to pine and fir forests west of Mexico's capital.
In contrast to Rickards' view, Tierra Curry, a senior scientist at the Center for Biological Diversity, wrote that "scientists were expecting the count to be down slightly, but this level of decrease is heartbreaking."
"More protections are clearly needed for this migratory wonder and its habitat," Curry wrote.
Environmentalist and author Homero Aridjis said that "the decline of over 53% of populations in the butterfly reserve is worrisome, above all because of the effects of climate change on the migration route and on the wintering grounds in Mexico."
Aridjis said crime and deforestation in Mexico is also a cause for alarm. One butterfly activist and a part-time guide in the reserve were murdered earlier this year.
Last year's numbers were the biggest since the 2006-2007 season. Two years ago, the butterflies covered 2.48 hectares (6.12 acres), similar to this year's numbers. The butterflies hit a low of just 0.67 hectares (1.66 acres) in 2013-2014.
Mexico has made some strides against illegal logging in the reserve, but Aridjis said it remains a problem in some areas. Butterflies depend on health tree canopy to protect them from rain and cold.
Some scientists said the approximately 6-hectare (15-acre) coverage of a year ago should be seen as a minimum for the viability of the migrating monarchs in the future.
Loss of habitat, especially the milkweed where the monarchs lay their eggs, pesticide and herbicide use, as well climate change, all pose threats to the species' migration.