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Most of Papua has a fairly uniform climate year-round: hot, humid and rainy in the lowlands, cooler or even downright cold (at night) but still humid and possibly even more rainy in the mountains. As such, unless you are going for diving maybe, weather should not be a huge concern when trying to time your visit - pretty much any time of the year will be as good as any other. If still trying to choose based on this, in most of Papua it tends to rain a bit more during the northern hemisphere's winter, just like in the rest of Indonesia. The area around Merauke is the only one where this difference is really marked though. On the other hand, the area around Sorong, including the Raja Ampat Islands, tends to follow more the weather pattern of Central Maluku, with more rain during the northern summer months.
You can find actual weather statistics on the following websites:
World Weather Information Service offers a very clear chart for only one place in Papua:
Weatherbase offers less clearly presented, but more detailed and useful date for:
For the really concerned, Weather Underground offers the most detail, and on the largest number of places. You can find current weather conditions, short term and extended forecast, and most interestingly even detailed data on actual weather conditions from the past years for the following places:
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