Sharma, who is already under judicial custody, was produced before a special court in Mumbai, which remanded him in NIA custody till January 19, police said.
"Sharma was produced before the court which remanded him in NIA custody till January 19," said special NIA Prosecutor Rohini Salian.
With Sharma's arrest, the number of accused held in connection with the 2006 Malegaon bomb blasts has reached 4.
The multiple bomb explosions in Malegaon, a communally sensitive powerloom town in Nashik district in northern Maharashtra, about 200 km from Mumbai, had occurred near a mosque on September 8, 2006 killing 37 people and injuring over 100.
After the blasts, the Maharashtra Anti-Terrorism Squad had arrested nine suspects. However, the MCOCA court had granted bail to all of them on November 5, 2012.
The probe into the blast was handed over to the Central Bureau of Investigation, which endorsed the ATS findings. The case then went to the NIA, which came into existence in 2009, post the 26/11 Mumbai terror attacks.
In November last, the NIA had told the court that the confession of Swami Aseemanand, arrested in 2007 Hyderabad Mecca Masjid bomb blast case, pointed at the involvement of a right-wing group in the Malegaon attack.
Malegaon had seen another attack in 2008 allegedly by rightwing Hindu groups. Sadhvi Pragya Singh and former Lt Col Srikant Purohit had been arrested in connection with the blast.