Cold, disease and malnutrition were the biggest killers and relief groups said they could not reach areas cut off by snow to help after the poverty-stricken province of Ghor was hit by the harshest winter in a decade.
"Several hundred to a thousand would be a low estimate of the number of children that could have died," Paul Hicks, programme director western region Afghanistan for Catholic Relief Services said in Kabul on Friday.
Afghan and UN officials have said that the cold snap had claimed at least 267 lives in Afghanistan in the past month, many of them children. Thousands more people are thought to be stranded in remote areas.
Hicks said a 10-person team from his organisation had hiked to 16 villages which had been snowed in and had found five children had died in each hamlet in Ghor's Sharack district.
"Eighty children died last month - most in the last 10 days or two weeks and what is getting them is the cold and lack of food, because they are already undernourished due to the drought," Hicks said.
"It is a serious challenge - if not taken care of, it will cause a human catastrophe"
deputy provincial governor
Afghanistan has suffered from a lengthy drought in recent years which has caused misery for poverty-stricken farmers and people throughout rural areas.
Hicks said his team had reached only a fraction of the 250 villages in Sharack district alone and had not been able to get through to any others in neighbouring Tulak and Saghar districts.
Deputy Provincial Governor Ikramuddin Rezaie said that tens of thousands of people were facing a food shortage in remote villages.
"It is a serious challenge - if not taken care of, it will cause a human catastrophe," he said.