We are never told the answer to this question in Martel's novel. In reality, the answer is unimportant. That is Martel's whole point. What IS important is the story itself.
If you want to explore these points further, it helps to reread the last five chapters of the novel. In these chapters, Pi Patel retells the entire story you have already read. He then experiences the disbelief and chagrin of the two Japanese men from the Maritime Department. Eventually, Pi gets extremely frustrated:
I know what you want. You want a story that won't surprise you. That will confirm what you already know. That won't make you see higher or further or differently. You want a flat story. An immobile story. You want dry, yeastless factuality.
Immediately after that statement, Pi give the two men exactly what they want. He gives them a "flat" and "immobile" story bereft of animals. If you want to stick to this theory, then you could go so far as to say that Pi did, in fact, give them "yeastless factuality."
In reality, though, the importance of the entire novel comes within the next few paragraphs:
Pi Patel: "So tell me, since it makes no factual difference to you and you can't prove the question either way, which story do you prefer? Which is the better story, the story with the animals or the story without animals?
Mr. Okamoto: "That is an interesting question..."
Mr. Chiba: "The story with the animals."
Mr. Okamoto: "Yes. The story with animals is the better story."
Pi Patel: "Thank you. And so it goes with God."
These statements are thick with meaning. According to Pi, it doesn't matter how God reveals "His" story (through Catholicism, Islam, or Hinduism). Divinity remains the same, regardless of the limitations of human knowledge and language. According to Pi, God simply changes the story in order to reach different kinds of people all over the world.