Hundreds of conservationists decided not to take part because of fears prompted by comments from a minister that the survey will be used to seize elephants and send them to temples for use in religious ceremonies.
Some 4,000 people are taking part in the two-day survey which is the first time formerly war-ravaged Sri Lanka has attempted to count elephants in all of its national parks
The enumerators headed out before dawn on Friday and started the count at watering holes, ancient irrigation tanks and lakes commonly used by elephants.
The animals will be categorised according to gender and the number of young, Pradeep Hettiarachchi, park warden at the Minneriya National Park told AFP.
"We have the largest concentration of wild elephants in a single park and the survey will give us valuable information for park planning and conservation work," Hettiarachchi said.
The boycott was triggered by reported comments by Wildlife Minister S. M. Chandrasena earlier this week who said that the