PayPal is of the largest global payment gateway solutions. They operate in almost every country including Malaysia. It is easy to use and set up. PayPal has a very powerful API which can be used to customise the payments based on the merchants requirement.
eGHL (GHL Solutions) is a secure internet payment solution that covers both cards & non-cards payments channels in Malaysia charges the lowest transaction fees. It has two plans – Starter and Small Business. The starter planPayment Gateways (Malaysia)
Your need for two-factor authentication feature can be met by Paypal and 2checkout who provide this feature in Malaysia. For more details and a comparison between the two, visit: http://www.analyzo.com/compare/299/8,9,Payment Gateways (Malaysia)