Union Home Minister Rajnath Singh and former chief ministers Ghulam Nabi Azad and Omar Abdullah were among those who received the body at the Srinagar airport along with his family members and relatives.
The leaders flew in on an earlier flight. Sayeed's body was flown from Delhi in a special Indian Air Force plane.
The Jammu and Kashmir has declared a week-long mourning and a holiday on Thursday.
Sayeed's cabinet colleagues and senior civil and police officials were also at the airport, where a guard of honour was presented to the departed chief minister.
"A 'Nimaz-e-Jinaza' (funeral prayer) will be offered at the Sher-e-Kashmir cricket stadium after which the body will be taken to the chief minister's official residence," a senior PDP leader told IANS.
The body will be then taken to Bijbehara for burial at Sayeed's ancestral graveyard.
A high alert has been sounded throughout Jammu and Kashmir in the wake of Sayeed's death on Thursday morning in New Delhi's All India Institute of Medical Sciences.
Heavy deployment of security forces was made all along the 45-km road from Srinagar to Bijbehara town, situated on the Srinagar-Jammu highway.