The attack, whose motivation remained unclear, was claimed by the "Lizard Squad", a group that has taken credit previously for denial-of-service attacks around the world.
It was not clear why the troubled airline was targeted, but the Lizard Squad said on its Twitter feed that it was "Going to dump some loot found on malaysiaairlines.Com servers soon."
Visitors to the website were re-directed to another page bearing an image of a tuxedo-wearing lizard and reading "Hacked by LIZARD SQUAD - OFFICIAL CYBER CALIPHATE".
Media reports said versions of the website takeover in some regions included the wording "ISIS will prevail".
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Normal access to the site appeared to be restored later today, but it marked another bout of bad press for the beleaguered national carrier.
The unexplained loss of MH370 and the airline's poor handling of the crisis severely damaged public confidence in the carrier, sending business into a tailspin.
A few hours before the website was restored, Malaysia Airlines had released a statement confirming its Internet domain name had been compromised, re-directing users to the dummy page.
"At this stage, Malaysia Airlines' web servers are intact," it said.
"Malaysia Airlines assures customers and clients that its website was not hacked and this temporary glitch does not affect their bookings and that user data remains secured," it said.
However, the hackers disputed that, releasing on Twitter what appeared to be a screen grab of some airline data including reservations.
The Lizard Squad is a group of hackers that has caused havoc in the online world before, taking credit for attacks that took down the Sony PlayStation Network and Microsoft's Xbox Live network last month.
The extent of any links with the Islamic State, however, are not known.