If necessary, from Indonesia it is easy to get to Malaysia (and vice versa). The easiest and fastest way, traditionally, is an airplane. The capital of Malaysia, Kuala Lumpur, regularly leaves from Jakarta (2 hours en route), Medan (1 hour), Pekanbaru (from this city you can fly to Malacca), Padang, Bali (3 hours en route) etc. Departures are operated by Malaysia Airlines, Air Asia, Lion Air, KLM.

Those who are not looking for easy ways can get from one country to another by bus, running from Malaysian Kuching to Indonesian Pontianak. The visa is not issued at the border point, so it should be taken care of in advance. This is the only option to cross the border by land, there is no railway communication between the countries.

But from Indonesia to Malaysia you can get to the ferry. They go daily on the routes Medan - Penang, Think - Malacca, Riau - Johor Bahru, Tarakan - Tawau and some others. Also between the islands are frequent cruising speed boats, so to reach, for example, on Sumatra from Port of Klang or Penang, there will be no problem.