I would like to help a few non-profit organizations to setup a web site that can accept membership fee and donation online.

I think most of the Payment Service Providers do not accept such application.

Any suggestion, besides using PayPal?

You can try 2CO or WorldPay.
Or, just use local bank online banking services if the donators are from Malaysia.

Found that Maybank start to send payment receiver an email on Maybank2u online fund transfer. Good feature! I do not need to check account manually and can know who bank in the money

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LiewCF | Malaysia Bloggers Forum

nice topic indeed....

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My Blog | Malaysia Bloggers

use maybank account should be good for Malaysian.

Donor can pay via ATM to the account. And don't think there is charge(someone confirm?)

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Malaysia Property | Funny Junk | Internet Marketing

Use Maybank2u if majority donors from Malaysia...

I like the second layer 'check' feature...so-called TAC (Transaction Authentication Code). Double check so you won't lose ur money easily

I used this as a gateway for fundraising Charity Fundraising