Malaysia to Papua New Guinea by motorcycle?

Through to West Timor/Timor Leste is the more common route - I've done bits of it, but not the whole shebang. I've ridden all over Bali, Lombok, Sumbawa and Flores - both by scooter and car.

You can overland into PNG but you need to get a visa before hand.

Some questions for before you put your gloves on.

1) Do you already have a bike? In Malaysia? Do you own it and have the books for it? Assuming yes, yes, yes and yes you'll need to ferry it over to Indonesia - there are plenty of options for this. Google is your friend.

2) If you don't have a bike and plan to get one in Indonesia, you'll need to buy one in Indonesia as nobody sane will rent you one to ride it to Papua! To be "legal" and for insurance purposes an international driving permit for riding a bike is advisable. If you drive unlicensed you can expect to be fined repeatedly and any insurance you have will most likely be void in the event of an accident.

Ok, once that is sorted out, the base route (very broad strokes):

Across Java -> ferry to Bali
Across Bali -> ferry to Lombok 
Across Lombok -> ferry to Sumbawa 
Across Sumbawa -> ferry to Flores 
Across half of Flores -> ferry to Kupang (West Timor) 

I wouldn't characterise motorbiking in Java as "extremely dangerous" but I would say you need to be mindful of trucks and remember your place in the vehicle pecking order (near the bottom, above pedestrians). Most people I know who have ridden extensively in both find the Balinese traffic far more challenging than Javanese, but your mileage will vary.

In the East, on Lombok and especially on Flores, Sumbawa, Sumba (if you divert there) and Timor, riding late afternoon and especially in the evening is not recommended, as there is a substantial chance you will be robbed. Do not ride at night unless it is absolutely unavoidable.

Traffic in the east however is extremely lights - I've ridden for hours in the middle of the day on Sumbawa without seeing another vehicle. You won't have that problem in Java ha ha.

Time-wise, 3-4 months at a comfortable pace, which means you'll need to allow for a visa run out to Malaysia to get a new tourist visa.

Is it possible, yes (assuming you don't mind ship / ferry crossings thrown in). Will it be easy, no.

95% of your ride will be through Indonesia, working your way down the main islands of the archipelago, then some longer ship crossings to reach West Papua. There is only one overland border crossing from West Papua into Papua New Guinea and that is on the northern coast between Jayapura and Vanimo. The road from Vanimo to the rest of PNG is unknown to me, but apparently exists.

You can look up some of the ship crossings with Pelni, one of the major shipping / ferry players: https://www.pelni.co.id/welcome

@Tom's answer seems to address your question well re actual routes and modes.
This response focuses on different but vitally important aspects of such a journey.

The Malaysian peninsula is "safe enough" for motorcycles if you are experienced in multi-country travel.

Travel in Java Indonesia is extremely dangerous for motorcyclists.
If you are competent and careful and take things slow and steady and assume that all the drivers who are out to kill you are out to kill you and that any of the rest may do so anyway then the journey is probably just "very risky".
You'd at a minimum want good health and vehicle insurance cover, with certainty that it applied to ALL conditions and areas en route.
You'd also need to personally accept the risks of potentially low availability of medical facilities and evacuations times of up to some days in worst case areas in Java. I have no direct knowledge of the conditions in IJ/WP but would expect them to be worse than Java in many cases and ~= "just accept that you'd probably die" worst case.

You can find many accounts of local motorcyclists being killed or maimed on Indonesian roads in Java/Sumatra/Borneo. Accounts of bad things of any sort in WP/IJ can be harder to come by. (Do not be encouraged by this aberration).

When I was in Yogyakarta I inquired re hiring a small motorcycle from a man who hired out motorcycles - with the aim of riding to Bali (except for the wet bits). He refused the hire point blank. No matter what the financial protection given him he did not think it worth his risk, or mine.

I do not know about motorcycling conditions in West Papua / Irian Jaya but while traffic may be less, I imagine that general hazard level would be high.

A more problematic issue for travel in WP/IJ may be the political constraints. While permission for access to Java and Sumatra is easily enough obtained, access to IJ is much more tightly controlled and you may be denied access unless you have a good reason for the journey and are 'politically acceptable' to the authorities. YMMV.

Ask an expert:

All that said, if you are genuinely keen, I can refer you to a friend who has ridden a one lung Royal Enfield 500 through a large number of countries (including East Timor). Hospitalised once - broken bones after she met a 4wd head on on a remote Asian jungle trail - flown back to UK for repairing and picked up bike and continued many months later. VERY experienced international motorcycle traveller. See my profile for email address.

__________________________

Pedants corner:

Some have suggested that "riding" the route is impossible due to the various bits of water along the way.
Here are some people who seem to have done similar and who have no problem with the terminology. The text given is a direct copy in each case. Bolding added for clarity.

Bicycle

• BLUFF TO CAPE REINGA Follow my bike ride starting from the Bluff on March 2nd 2010 and arriving at Cape Reinga 21st March 2010....a total of 2,257km's When riding the length of the country, I hope to raise funds for The North Shore Hospice. Visit: http://www.fundraiseonline.co.nz/blufftocapebikerideforhospice/

Car

• Cape Reinga to the Bluff: Driving across New Zealand

Tramping / trekking / hiking

• Tramping (Trekking) the Length of New Zealand -- Route, Photos, and Journals

Tractor!

• Retiree to drive from Bluff to Cape Reinga by tractor for good cause

EV

• A Far North man attempting to make motoring history by driving his electric car from Cape Reinga to Bluff and back is on his return journey and should be home by Christmas.

____________________________

All the above routes cross, without qualification of the journeying term used (drive/trek/...), the wet bit in the middle - named "Cook Strait". This is about as real a water crossing per distance as you can find.

I travelled from West Papua to PNG a couple of years back. The only real border crossing is from the Jayapura to Vanimo. I had to pay a "fine" to to exit Indonesia from West Papua and had to walk about one kilometre between the border checkpoints of the two countries.

In PNG you would need a durable bike - few roads along the north coast were paved when I was there, some were pure mud. Also, you would have to cross some rivers one way or another. You can probably drive most of the north coast on loggers roads or take ferries to hop some distance if necessary. I travelled on the back of pickup trucks loaded with coffee and cocoa beans most of that stretch. In the east of the country there are fairly good roads that connect to the highlands. I don't know how easy it is to get from there to Port Moresby however.

Obviously, be careful. There are plenty of scary PNG travel stories you can read up on. Nevertheless, most people I met during my trip were really friendly can hospitable!

I can add that travelling on a motorcycle on Bali and Flores is an excellent way of travelling. Bali however is very busy and one big traffic jam. This year I travelled on a rented motor-scooter on Flores from Maumere to Labuan Bajo (east to west, 850 km with all side trips). There is no better way to travel Flores, the Trans Flores 'highway' (ahum...) is excellent, really. I encoutered one landslide and had to wait for half an hour. Outside the villages there's not much traffic. I noticed the Australian governement funded roadworks.

You don't have to worry about safety, people are very friendly and open. Be aware that most of the road on Flores has no straight stretches, it's all bends, so speed will average at 60 or less. Most annoying thing are the chickens and roosters who will do their best to commit suicide by trying to get in front of your motorbike.

Haven't been to PNG so can't tell. Bali and Java are more crowded/busy. Malaysia Peninsula, excellent roads and perfect for motorbike. You can take ferrys between the Islands, they run regularly. There's more than the Pelni lines between the neigboring islands.

The local truck- and (mini)bus drivers don't mind driving 14 hours or more in a row staying awake on red bull drinks and alike. That is a serious risk to stay alert for. Besides enjoying the country, islands and experience, this also is a good reason to slow down and take more time, do short stretches and stay alert.

There is no land connection between Malaysia and Papua New Guinea. So, no. Unless your motorcycle flies, you cannot ride from one country to the other. You would need to ship your motorcycle either by land or sea to get to the island of New Guinea.

Malaysia consists of a peninsula on mainland Asia and the northern part of the island of Borneo. Papua New Guinea is the eastern half of the island of New Guinea. (The western half the are Indonesian provinces of Papua and West Papua.) Borneo and New Guinea are about 2500+ km apart, separated by the Pacific ocean.