This question has been debated both in the Edo Period and in modern times. There are a lot of inaccurate books regarding Musashi in English. The following information comes from one of the more reliable books on his life: Miyamoto Musashi: His Life and Writings by Kenji Tokitsu. He discusses this point, pp. 79-80.

The wooden sword Musashi used was particularly heavy and measured 1.26 meters in length. On the reasons for his using this wooden sword, Hirayama Shiryu-gyozo (1759-1828), a sword master, wrote in his work "Discourse on Swordsmanship"(Kensetsu):

Ganryu Sasaki Kojiro used a sword whose blade measured ninety centimeters in length. It was nicknamed "the clothes-drying pole." Judging that it would be to his disadvantage to use two swords, both of which were shorter than that of his opponent, Musashi asked the boatman to give him an oar, from which he made a large wooden sword. With that he could kill his adversary by smashing his skull. Musashi's talent was this ability to change his means as appropriate for a given adversary.

Tokitsu himself doesn't buy this explanation, since Musashi's real sword was also long, more than ninety centimeters. His own personal opinion is that

Musashi wanted to fight with a weapon whose length was greater than Sasaki Kojiro's and he carried out his strategy in such a way as to conceal it until the last moment. Initially he kept the end of his weapon immersed in the water, putting his back to the sun. Then, during the combat, he held it at an angle over his shoulder.

But he admits that this is just a guess. There's not enough information on how the fight went down to know what Musashi's strategy was. The only source based off an eyewitness's testimony doesn't comment on that, or give the details of the fight itself, just its result.