Special Maharashtra Control of Organised Crime Act (MCOCA) judge V V Patil framed charges against the accused under eight counts.
"All the accused pleaded not guilty and said they will face the trial", Special Public prosecutor Pradeep Gharat said.
The 12 accused are among the 14 Pujari gang-men, who were arrested between November 15 and 21, 2014.
Following their arrest, the city police had claimed to have thwarted a plot to kill Bhatt and also cracked the case of firing in the air outside the residence of Karim Morani, producer of Bollywood film "Chennai Express".