The VOC, as has been stated above, started off as a commercial and maritime enterprise. The original setup was simple: sail a fleet to Asia, buy spices, sail back, sell spices at the highest possible profit, and equip another fleet to do the same. By implication, VOC warfare started off as being naval.
Although the pre-VOC fleets as well as the first VOC fleet did not have explicit military goals, they certainly did go armed. In Europe, trade was also quite a violent activity in these times. Merchant ships trading within Europe always went armed, as piracy was rife and market competition was practiced by coercion and violence as often as not. The Dutch fleets sailing to Asia not only had to be prepared for what might await them on the other side of the Cape: they might run into trouble with Spanish fleets before they had even left European waters.
Once in Asia, their military preparations did not turn out to be wholly unjustified either. In an article on the violent nature of Asian society, Ricklefs turns the usual argumentation around and states that if the VOC wanted to get anything at all done in Asia, it had no choice but to use violence. The Asian societies it encountered were no more peaceful than what it was used to back home.  The first Dutch fleet rounding the Cape, in 1595 under the leadership of De Houtman, found itself in a naval battle with the Bantamese off the coast of Java, after a trade conflict and mutual suspicions between the Bantamese and De Houtman got out of hand. A naval battle ensued, which the Dutch, by the use of their cannon, managed to win.
In the literature there is some discussion about whether Asian societies were at all interested in naval warfare: we can say that at least some certainly were, witness the maritime power projection of the Makassere and Achinese, or the naval wars between Korea and Japan. However, there does not seem to be any doubt that European warships were superior to anything they encountered in Asia. Two centuries of intense naval warfare on the seas of Europe had led to technological innovations which had no counterpart in other parts of the world. “Sails and guns” had in steps been substituted for “oars and warriors”, dramatically increasing the damage that a given number of sailors could potentially inflict. The East Indiaman, which was a relatively low, long and manoeuvrable gun platform, yet at the same time could do excellent service as a merchant vessel, was an exponent of these developments. In practice, it turned out that Asian war fleets could not match the standard of these European ships. Here, then, was one of the innovations of the Military Revolution that could be exported, and which did give Europeans an edge over Asian adversaries.
The centralization of the VOC administration in Asia, as well as the increasing number of ships that the VOC had operating in Asian waters, led to what many authors describe as a maritime hegemony of the VOC, as early as halfway into the 17th century. The VOC ruled supreme at sea, both with respect to other European colonial powers and towards the Asian societies it encountered. The VOC put this maritime military hegemony to good use, for one by blockading Goa from 1636 onwards in order to disrupt the Portuguese enterprise throughout the Indian Ocean, for another by blockading Suratte in order to enforce different trade terms, as has been described above. In addition, this maritime hegemony also had its political effects on the VOC’s neighbours, particularly in the island world of the Indonesian Archipelago. The maritime hegemony resulted in the Javanese Mataram state slowly losing control over its overseas areas, and thus interrupted its state formation process. It also gave the VOC the power to keep the Mataram state from hiring mercenaries from overseas. As, in the explosive and dynamic political system of the Mataram state, the prajurit, i.e. the professional warriors from the noble classes of Javanese society, were prone to change sides and therefore very unreliable, the Javanese leaders always preferred to hire Buginese or Balinese mercenaries. With the advent of Dutch maritime hegemony, however, this supply was at the mercy of the VOC. Thus, the ability of the Susuhunan to wage war was considerably hampered by the fact that the VOC ruled the waves.