Kumar was promoted to the rank of Dy. Inspector General of Police in 1993, after which he proceeded on deputation to the Central Bureau of Investigation where he served until 2002. In the CBI, he dealt with a wide variety of cases involving terrorism, organized crime, economic offences and corruption. He led the investigations in the serial blasts which took place in Mumbai, which were handed over to the CBI by the Mumbai Police in Dec. 1993.
Under his leadership, the Special Task Force (or STF, created in the CBI to investigate the case) arrested seven members of the Memon family and sixteen other absconders. The charge sheets filed, at the time by the CBI led to the conviction of 100 out of the 123 accused in the case. Under his leadership, the STF also cracked the serial train blast cases of 1994, which occurred on the first anniversary of Babri Maszid demolition in various prestigious trains, and unearthed a terrorist outfit called Ahle Hadees. The trial ended in life sentence to all the fifteen arrested accused.
His tenure in the CBI is also highlighted by the solving of the Meenakshi Amman Temple Blast case of Madurai, the unearthing of the UTI Scam, the arrest and deportation of American Center attack mastermind Aftab Ansari from Dubai, the arrest of Abdul Lateef, a notorious underworld don of Gujarat; Romesh Sharma, a Dawood Ibrahim henchman masquerading as a politician based in Delhi; and the cracking of the Cricket match fixing scandal. Jagtar Singh Tara, the first accused to be nabbed in the assassination of the then Punjab CM Sardar Beant Singh, was arrested by him, which led to the unravelling of the entire conspiracy.