A dozen privately-run wildlife organisations on Tuesday pulled out their volunteers on the eve of the survey which aims to count the number of animals across all of the formerly war-torn island's national parks for the first time.
Wildlife Minister S.M. Chandrasena told reporters on Monday that the data would help to identify suitable elephants that could be domesticated and sent to Buddhist temples where they are used in ceremonies.
"Calves suitable for pageants will be chosen during the elephant census, tamed and handed over to the temples," Chandrasena said, according to the Colombo-based Daily Mirror newspaper.
"Sometime back there were more than 300 tamed elephants in the country and the number has now dwindled to around 150 of which only a few are tuskers suitable for pageants."
While the Department of Wildlife Conservation moved to deny the minister's comments, elephant conservation groups on Tuesday voiced their disgust over a "calculated" move to tame wild elephants.
"Capturing wild elephants or tuskers is harmful for the natural breeding process in the wild," conservationist Rukshan Jayawardene told reporters on Tuesday.
He said some 12 groups representing over 100 volunteers were pulling out of the survey until the government gave assurances that wild elephants would not be captured.
Wildlife Department director general H. D. Ratnayake said he was not aware of the minister's directive. "The survey is not to capture elephants, but to assess their numbers for conservation work," he told AFP.
Over 4,000 workers and volunteers were expected to fan out for two days from Friday to count and categorise elephants at watering holes across the Indian Ocean island.
The $210,000 project will cover for the first time national parks in the north and east that were out of bound for conservationists during the island's decades long war which ended in 2009.
The results are expected to give the most detailed picture yet of herd patterns and numbers in a country that boasted 12,000 elephants in 1900. The department estimates the current population at just 4,000.
"We plan to do a water hole survey, where elephants are counted when they arrive to drink water from lakes and reservoirs in the national parks," Ratnayake said.
Surveys in the past have been restricted to a few regions, excluding the former conflict zones that were battered during the war between government forces and ethnic Tamil separatists.
But critics point out that an estimated two-thirds of Sri Lankan elephants live outside national parks, according to the department, and conservationists have also questioned the methodology of the census.
Local expert Srilal Miththapala said there was a danger of double-counting and raised the practical problem of identifying the vast number of watering spots visited by elephants across the country in just two days of counting.
"Elephants can move stealthily over a short period of time from one water hole to another during the counting process," Miththapala told AFP. "You can't do surveys over two days."
Instead, Miththapala suggested dung counting and transects, a system of following patterns of elephant movement along a set path over a period of time, were more accurate.
"Over the years direct counting methods have failed in India, and they now use direct counting supported by transects and dung counts to compile their statistics," Miththapala said.
In India, there are an estimated 30,000 elephants in the wild.
Ratnayake said that over 200 elephants were reported killed by Sri Lankan farmers last year as they destroyed crops, while some 50 people were also killed in what are often described as "man-elephant conflicts".
"The elephant's long-term survival is linked to the welfare of people, with whom the animals share land. Elephant management has become a huge problem over the last few years," Ratnayake said.
The island's forest cover has shrunk to about 20 percent from 41 percent in the 1930s, according to the department.