Although there are large numbers of natural disasters reported in Malaysia, it is against a wide area as Indonesia is a large country spanning across few time zones. Natural disasters common here are the earthquakes, tsunamis and volcanic eruptions but very limited to the region that would be affected itself.
The crime rate in Indonesia has increased over the years but most are just petty thieving like robbery, theft and pickpocketing. Avoid showing your valuables and money in public and like most places in the world, be aware of your surroundings especially popular public places. There are several bombing reported at highly concentrated tourist area such as Bali and Jakarta, so as to minimize your risk, try to avoid tourist packed nightclubs or restaurants.
It is recommended to get vaccinated for hepatitis A and typhoid fever before traveling to Indonesia as food hygiene in some areas are questionable. Get more information in vaccinations for traveling in Indonesia.
Dengue is rampant in remote areas of Sumatra, Borneo and Lombok or points east, so bring strong repellants and be careful. Also the air quality in Indonesia is quite poor, especially in major cities, with occasional haze (June-October) from forest fires in Borneo and Sumatra, so if you have respiratory problems do remember to bring your medication and breather.
Areas to avoid
Maluku – there is serious civil unrest in this area with long standing communal tensions.
Papua and West Papua – political tension creates a high risk security situation in that area.
Central Sulawesi – security situation on risk due to religious tensions and terrorist activities.