Shipping lines say surge in the international crude price, which touched $136 a barrel on Thursday, has "forced" them to raise the rates since fuel is the second most expensive input in running a vessel.
From July 1, the new rate would be $1,695 for every TEU compared with the current $1,650.
India Pakistan Bangladesh Ceylon Conference (IPBCC), which represent member lines operating in this sector, have said they are increasing the bunker adjustment factor (BAF), also called bunker surcharge, to $415 for every TEU, starting from July 1. The present rate is $370.
Meanwhile, shipping lines connecting Indian ports with the US have also said that they will revise the BAF rates upwards by the end of the month.
Last month, freight rates from India to the US and Europe were increased by 60 per cent and 35 per cent, respectively.