Bangladesh will charge fees while allowing Indian vehicles to use its territory, Muhith told reporters Monday after a meeting with Indian High Commissioner Rajeev Mitter.
"We'll charge fees for capacity maintenance, as our infrastructure will be used by their cargoes," Muhith said a day after opposition leader Khaleda Zia told a political rally that India was seeking free transit.
Zia, also a two-term prime minister, has demanded that the Sheikh Hasina government scrap all deals that were signed in New Delhi in January.
Muhith said the government was working to frame new rules and fix the amount of fees to operationalise road and rail transit.
"It will take two to three months to finalise the rules."
The minister said the opposition's anti-transit stance is "political", The Daily Star newspaper reported.
Zia Sunday warned the government against giving transit to Indian goods. She threatened that no foreign vehicles would be allowed to use Bangladesh territory.
Muhith said Bangladesh has already been offering India limited transit through waterways as per the Protocol Agreement of 1972, and it receives around Tk 45 million ($639,849) in fees annually for maintenance of the routes.
Besides, it charges conservancy and pilotage fees, which take the total earnings from water transit to around Tk 200 million ($2,843,736) a year.
"Now we need a new set of rules for road and rail transport," said the finance minister.