iPay88 and Midtrans have the lowest transaction fees in Indonesia market. iPay88 charges a 3% transaction fee for VISA and Mastercard online transactions. If you’re using Malaysian online banking or E-wallets payment services, the transaction fees can be between 2-4%. iPay88 also charges one-time setup cost and a yearly fee of RM 488 (Malaysian Ringgit) and RM 500 respectively.
Midtrans charges a transaction fee of 3.2% + Rp 2500 (Indonesian Rupiah) on each transaction of card payment done online. For E-wallets, this transaction fee is Rp 3000/transaction. You can know more about payment gateways services for Indonesia market here: http://www.analyzo.com/search/payment-gateways-indonesia/350