The airline posted a net loss of 478 million ringgit ($150 million) for the quarter ended September 30, compared with a net profit of 233 million ringgit a year earlier.
It had earlier posted net losses of 242.3 million ringgit in the first quarter of 2011 and 527 million ringgit in the second quarter.
The company said fuel costs increased by 37.1 per cent in the third quarter from a year earlier while it faced an unrealised foreign exchange loss of 195 million ringgit compared to a gain of 88 million ringgit a year earlier.
"The operating environment for airlines in general remains challenging for the fourth quarter of 2011," group chief executive officer Ahmad Jauhari Yahya said in a statement.
"Not only is the jet fuel price staying high, the worsening economic situation in Europe is being translated into weak forward booking profiles for our long-haul routes."
Ahmad Jauhari said the airline was implementing a campaign to shut down loss-making routes while concentrating on higher-yielding flights in Asia, with the moves to begin bearing fruit next year.
In August, Malaysia Airlines and budget carrier AirAsia announced a surprise alliance that would eliminate head-to-head competition on some routes, allowing each to focus on their core markets.
Analysts have hailed the deal, saying Malaysia-based AirAsia will be able to concentrate on offering low-cost journeys, while Malaysia Airlines caters to more upmarket travellers.
The national carrier said that both airlines were presently working on several joint initiatives in training, ground handling, joint procurement and fuel efficiency.
What the stars mean:
★ Poor ★ ★ Promising ★★★ Good ★★★★ Very good ★★★★★ Exceptional