Besides boundary walls and toilets, children also spoke of corporal punishment and bullying, among their main concerns.
A survey in which at least 6,000 children across the globe participated has revealed that nearly one in every three children in India has concerns about their safety at school.
The "Small Voices, Big Dreams" survey, conducted by ChildFund International, captures the views of children, aged between 10 to 12 years, on education and safety at school in various countries.
The participating countries include India, Afghanistan, Cambodia and Zambia amongst others. The findings highlight striking similarities and differences between children in different parts of the world.
"While children almost universally agree that education is important, a third of respondents in India (28 per cent) expressed their school is safe only sometimes, citing deficient infrastructure and lack of toilets as their concerns," the survey said.
Besides boundary walls, first aid facilities and toilets, children also spoke of corporal punishment and bullying, among their main concerns.
In developing countries, 21 per cent of children said that being safe at school meant clean school buildings and facilities. This response has been highest amongst children surveyed in India (58 per cent), Ethiopia (55 per cent) and Bangladesh (54 per cent).
In India, children defined safety at school as having a clean and safe building (58 per cent), having proper preventive security measures in place (46 per cent) ranging from "out of bound" areas, to protection from strangers and supervision by teachers.
About 23 per cent of children described feeling safe as not being the target of physical, emotional abuse or violence, including, as many children said, corporal punishment and "no bullying".
Almost two-thirds of children in developed countries (64 per cent) said education is important compared to 40 per cent in developing countries and 45 per cent of respondents in India.
"This survey tells us that children in India are passionate about bringing in a more interactive approach to learning and subjects that would prepare them for real life, like technology. But it is alarming to know that safety in their institutions is a grey area," National Director of ChildFund India Neelam Makhijani said in a statement released on Wednesday.
"We can't lose sight of the fact that every child has the right to learn in a safe environment and a collective intervention is our moral responsibility," she said.
According to the survey, children also have many ideas about how they would improve the education system in their country if they were in charge.
Children in India are interested in creating high quality learning environment, modernising class curriculums to widen the range of subjects available, and make learning more interactive and fun by including sports and creative arts, and greater student participation.