The Nilame has taken the elephant calves to Kandy with the support of about 50 police and army personnel after hours of battle during which the baby and mother elephants have been injured.
Officials at the elephant orphanage say the two baby elephants, the only tuskers among 50 other calves, are not even three years old and they are not usually separated from their mothers until at least they are five years old as they mostly depend on the mother's milk.
Health of the injured mothers is now threatened as they are still lactating and pining for their offspring, the officials say.
The chief prelates of Malwathu and Asgiri Chapters of the Temple in a joint statement however denied the reports of inhumane transfer of the baby elephants and said they were gifts to the temple.
Earlier this month Sri Lanka Cabinet approved a request by the Minister of Sports and Public Recreation Gamini Lokuge to gift two baby elephants belonging to National Zoological Department from Pinnawala Elephant Orphanage to Malwathu and Asgiri chapters as there is a shortage of tuskers to employ in traditional religious festivals.
However, the sources say the anger has sparked not from the act of donation but from the inhumane way of removing the baby elephants from their mothers.
According to biologists elephants typically are fully weaned at around 5 to 6 years of age but the process may take up to 10 years. They say if they are taken away sooner they will not learn social skills to cope and will suffer from malnutrition, stress and disease leading to early death.