The charity said its aid workers recently saw armed forces using bulldozers and large vehicles to destroy shelters and schools in the Somali capital, Mogadishu.
Most demolished properties housed families who have fled fighting and drought in parts of the country.
World Vision, along with 82 other agencies, have issued a statement calling on the government to protect housing, land and property belonging to internally displaced people (IDP).
The statement said the operation has left thousands of vulnerable families homeless and without water, food, health services and community infrastructures such as latrines and schools.
Simon Nyabwengi, National Director of World Vision Somalia, said: "Over 21 IDP settlements, housing over 5,800 households were destroyed.
"The destruction included schools, learning centres and materials leaving children not only homeless but also with no hope to access any form of education.
"These communities, who are displaced as a result of drought, are now faced with further vulnerabilities and risks including disease outbreak, exploitation and abuse."
The charity explained its concern for families who did not have enough notification of the operation and urged Somali government to provide the families with viable relocation options that are required by international law.
The ongoing drought and conflicts in Somalia continue to displace people. Last year more than one million people were displaced, living in settlements across the country.
The drought is set to continue this year, leading to more people seeking life-saving humanitarian support in settlements.
