Union Home Minister Sushilkumar Shinde said here that "the body has been buried according the jail manual and there was no way it could be handed over".
Omar had, in his letter to Prime Minister Manmohan Singh last month, demanded the return of the body of Afzal as well as that of Maqbool Bhat who was hanged in 1984.
The home minister told reporters here that Guru' family can come and pay respects at his grave in Delhi.
Afzal Guru was hanged on February nine and his family was informed through a speed post communication which was delivered to them two days after the execution.
To a question on taking action against Jammu and Kashmiri separatist leader Yaseen Malik sharing the dais with Lashker-e-Taiba founder Hafeez Saeed in Islamaabd, Shinde said "the government has taken note of the development and action will be taken at an appropriate time."