Indian officials say the youths were killed in a crossfire Wednesday as Indian troops battled militants in the Kupwara district of northern Kashmir.
But demonstrators accused Indian soldiers of firing indiscriminately at the boys as they were playing in a park in the village of Doodipora.
India's chief minister for Jammu Kashmir state, Ghulam Nabi Azad, has ordered an investigation.
In other violence Wednesday, Indian security forces raided rebel hideouts in the Udhampur and Poonch districts of Indian Kashmir. Indian officials say seven militants were killed, along with two Indian security personnel.
Indian Prime Minister Manmohan Singh is to hold talks with Kashmiri political leaders on Saturday. But several prominent Kashmiri separatists say they will not attend.
Some information for this report was provided by AFP, AP and Reuters.