Afzal was hanged and buried in Tihar jail in Delhi on February 9 and there have been demands from his family that his body be returned to them.
"I had written to the PM on the 19th of this month asking for the return of the bodies of both Afzal Guru & Maqbool Bhatt to their families," Omar tweeted on the microblogging site Twitter.
Omar said he followed this up with a visit to the Prime Minister to make the request in person a few days ago. "My Govt will continue to raise this issue with Delhi," he said.
"I had hoped to avoid playing politics with the body of Afzal Guru but that seems to be impossible to avoid with the Mufti Sayeed letter now."
"I guess I should have played politics by making the letter public immediately but am glad the PDP has joined in support now," Omar said in a series of tweets.