The 78-year-old Ahamed died at 2:15 am at RML hospital where he was admitted yesterday and put on artificial life support.
"E Ahamed has passed away at 2:15 am. His body has been taken to AIIMS hospital for embalming (a method to preserve a corpse from decaying) as the facility is not available at RML," a senior RML doctor told PTI.
Ahamed's body will be taken to Kerala later today.
The MP from Kerala's Mallapuram suffered a cardiac arrest during the President's address to the joint sitting of Parliament yesterday.
Congress President Sonia Gandhi, party vice president Rahul Gandhi, leader of Opposition in Rajya Sabha Ghulam Nabi Azad, besides other party leaders had rushed to the hospital late at night and met Ahamed's family.
Ahamed's family had alleged that they were not allowed to meet the leader.