The Thimphu Thromde together with the Department of Forest and the Natural Resource Development Corporation Ltd, (NRDCL) are cutting down poplar and cypress trees in the city.
The trees emit toxic gases and were apparently causing health problems like skin diseases, eye infections and allergy to people.
The trees disturbing telephone and power lines and those leaning toward houses are also being cut down, forestry officer Shera Doelkar said.
The trees along the swimming pool area and the high court are already cut down.
Earlier, the city has uprooted willows and poplar in a move to remove all exotic species and plant indigenous trees like blue pine.