The agency said the trio along with others fraudulently refunded money in the accounts of those who were not entitled to any such benefit.
Income Tax officer Sanjeev Kumar (currently posted in Lucknow), former senior tax assistant Rakesh Kumar Singh and Anand Kanojia, who worked as a daily wager with the department earlier, were booked by the agency yesterday.
The CBI had carried out a preliminary enquiry in March which revealed that fake income tax refunds were prepared by the trio and another person Anand Bajpai (now dead) by using PAN numbers of 13 tax assesses.
"None of the 13 tax assesses had claimed any refund or submitted any application for rectification of their ITR," the CBI said in the FIR.