The incident occurred as Bhattarai arrived at the airport to leave for Brazil to attend the United Nations Conference on Sustainable Development slated for June 20-22, as the head of a 21-member delegation.
Students affiliated to the opposition parties Nepali Congress and the Communist Party of Nepal (Unified Marxist Leninist) on Monday afternoon called for Prime Minister Bhattarai's resignation showing black flags at the Tribhuvan International Airport, the Himalayan Times reported.
The riot police blocked the protesters, who pelted the PM's motorcade with stones.
Three persons were injured while two vehicles were vandalised during the clash between the demonstrators and the security personnel, police said.
Bhattarai has flown to Rio de Janeiro despite advice from diplomatic and political circles that the head of a caretaker government cannot truly represent the country reeling under political uncertainty.
On his part, PM Bhattarai defended his trip claiming that his participation at the international forum is indispensable, adding the conference offers an opportunity to highlight the problems facing Nepal and other environmentally vulnerable Least Developed Countries.
Altogether 150 heads of government are attending the conference, which marks the 20th anniversary of the United Nations Conference on Environment and Development held in Rio de Janeiro in June 1992.