Assistant Commissioner of Police (Crime) Mukund Hatote told PTI that the court on Friday rejected bail pleas filed by the 12 accused.
District and Additional Sessions Judge N M Waghmare also rejected anticipatory bail applications filed by the remaining 36 accused.
In June last year, the Crime Branch of Thane police unearthed the racket in dispensing of petrol at the pumps, which was done by tampering with dispensing machines.
The Thane police had also raided petrol pumps in 21 districts of Maharashtra and two petrol pumps in Odisha.
Subsequently 12 persons were arrested. They filed the bail applications, which were disposed of on Friday, the officer added.
Explaining the modus operandi, Hatota said the accused connived and tampered with dispensing machines at petrol pumps by converting the pulser card, mother board, control card, and keypad and dispensed less petrol and diesel to customers.