The competition watchdog said revised fees introduced by MasterCard and the MasterCard Members Forum (MMF) may still be too high.
Last September the OFT said the interchange fees set by MasterCard restricted competition and were like a tax on consumers.
MasterCard subsequently altered the system, but the OFT suspects the group is setting fees to counter costs associated with other things such as interest-free periods on credit cards.
"The OFT has launched an investigation into MasterCard's new arrangements for setting the fallback interchange fees that apply to all UK domestic transactions made using UK-issued MasterCard credit and charge cards," it said.
The MMF includes leading credit card issuers such as Barclays and Royal Bank of Scotland.