I'll extend Rashaja's advice to include never book any flight at all, domestic or international, from Air Madagascar's website - the main reason why it's more expensive is because the handling has been outsourced to an upmarket French travel agency, which at least gives the impression of having something of a free hand in deciding what its cut is going to be, and therefore what price it's going to charge the customer..
Not only can you not get the domestic discount if you book using this system, the prices quoted are, as Rashaja say, vastly more expensive. I must admit to wondering if Air Madagascar itself doesn't quote higher prices to the agency so that it recoups the amount it has to pay in commission - but of course that is pure speculation.
Methods which I have used and which work very well include:
Telephone bookings via the Air Mad Paris Call Centre - the phone number: +33 (0) 892 701 819
Using an authorised agent from the list you can access via the links More about us / our points of sales on the Air Mad website. As all tickets are now e-tickets, if you're using a credit card, the authorised agent you use doesn't need to be in your own country. I have had excellent results from Aviareps, the agent in München/Munich in Germany, who have often quoted me a price cheaper than Air Madagascar's own call centre in Paris. Their number is: +49 89 55 25 33 15 (the number on the website has an extra "5", but this is a typing error).
You can communicate with these people in English. Both will ask you to fax them a copy of both sides of your credit card, which I have done many times without having problems down the line.
A third method I use that is not available to you is to get friends inside the country to book my domestic flights for me. The reason I mention this is that the prices they get charged - without any mention of a long-haul flight - have usually been within a couple of euros of the discounted price you get when you book in Europe - which, to say the least, throws an interesting light on Air Mad's current pricing policy.
Good luck!