The 62-year-old is survived by his wife Achamma and two daughters, Renu and Sindhu.
Besides his mother tongue Konkani, he spoke English, Hindi, Urdu, Tamil and Malayalam.
Family sources said the final rites would take place at the Ravipuram crematorium. Until then, his body would be kept at his residence at Chilavanoor for people to pay their last respects.
A highly respected Indian Police Service (IPS) officer from the Jammu and Kashmir cadre, Raju passed away around 3.40 am at the Lake Shore Hospital, medical oncologist VP Gangadharan said.
He had been admitted to the hospital Monday following a lung infection but the condition suddenly turned serious, necessitating a ventilator.
Gangadharan, who had been treating Raju for about a year, said the end came due to "severe complications" in the lung.
Raju, who also served with distinction in the Central Bureau of Investigation (CBI), headed the operational wing of the Special Investigation Team (SIT) formed to track down the killers of former prime minister Rajiv Gandhi in 1991.
Raju earned his first laurels as a CBI officer in Kerala in 1983-89 when he solved some dragging corruption and murder cases.
He was posted in the Kashmir Valley when militancy erupted. After his stint in the CBI, he returned to Jammu and Kashmir before finally heading the NIA.
Over the years, Raju was recognised widely as an expert on terrorism and counter insurgency and as an authority on the Liberation Tigers of Tamil Eelam (LTTE). He was an active member of India's strategic community.
Born July 27, 1949, Raju worked with a bank - where he met his future wife - before joining the IPS in 1975.
Raju served as the senior superintendent of police of Jammu district, as deputy inspector general in South Kashmir Range and as inspector general in Jammu.
At the SIT, he headed the team that proved beyond doubt the involvement of the LTTE in the conspiracy to kill Gandhi at an election rally near Chennai in May 1991.
It was Raju who signed the Indian government orders seeking from Sri Lanka the extradition of the now dead LTTE chief Velupillai Prabhakaran.
SIT chief D.R. Karthikeyan and Raju were the joint authors of "Triumph of Justice - The Rajiv Gandhi Assassination - The Investigation", a book which meticulously details how they cracked the Gandhi case.
After serving the SIT for years, he was posted as inspector general of police in Jammu and Kashmir in 1998.
He had another stint with the CBI later and became in 2002 its joint director.
After retirement, he took an active role in addressing members of the strategic community and think-tanks on issues related to terrorism and security. He also wrote extensively on security issues.
Only last month, the Central Vigilance Commission (CVC) inducted him into its board to assist the CBI in cases of fraud.
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