The body, covered with the national flag, was brought to the Masjid for the burial around noon and hundreds had converged to pay their last respects to the leader.
Kerala Ports Minister Kadanapally Ramachandran, KPCC President V M Sudheeran, Kannur MP P K Sreemathy, besides a host of IUML leaders were among those who were present at the masjid.
Kerala Chief Minister Pinarayi Vijayan had paid his respects at Kozhikode last night.
Prior to his innings in Parliament, Ahamed had served five terms as member of Kerala Assembly from 1967-91 and was Industries Minister in the K Karunakaran cabinet from 1982-87.
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He had served in the Manmohan Singh cabinet from 2004-12 as Minister of State for External Affairs and Railways besides holding the additional charge of the Ministry of Human Resource Development.
Ahamed, a widely travelled politician, had represented India in United Nations 10 times.
He was also an active member of the Union government's Haj Committee and also co-chairman for the high-level monitoring mechanism of India and Qatar in 2011.
The leader died at 2:15 AM yesterday at the hospital.