Compared with much of the region the transport system in Malaysia is a dream.
There are several rail routes around the country that have adequate sleeper trains and provide a great way to see the country, particularly if you enter from Singapore and want to travel up the east coast, or if you want to explore the west coast and move up into Thailand. Train travel is also reasonably cheap and safe compared to other countries in Southeast Asia.
Malaysia’s national carrier Malaysia Airlines has been plagued with bad publicity of late due to one of its planes being shot down over Ukraine and the other going missing en route from Kuala Lumpur to Beijing. To add to this, Malaysia’s low cost carrier AirAsia also experienced its own tragedy when one of its Indonesian planes crashed into the sea off the coast of Kalimantan. As such, travelers could be forgiven for being wary of plane travel in Malaysia, although it should be stressed that Malaysia has a far better aviation safety record than its neighbors such as Indonesia.
Bus travel is another key way that locals in Malaysia get around because it is cheap and while they also have better records than other countries there have been a number of incidents involving fatal crashes as well as fires on buses, and driving is not always of a high standard. Many long distance buses have toilets, televisions, and air conditioning but many do not, so check the bus you will be travelling on first before you buy a ticket.
Ferry travel is another way, sometimes the only way, of getting to many of the islands in Malaysia and as with the buses some of the boats are of a high standard and many are not. Check the boat first and make sure they have standard safety equipment like life jackets before you board.