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Fujimoto implies that she is the first and eldest of the sisters between him and Granmamere.
This is the answer to OP’s question… all the other replies are discussing events that happen after we see Ponyo is already bigger than the others.
First prototype, then mass production.
All that ham she’s been eating
Ham!
Wasn’t it that she had more magical ability than the rest, then got into all the potions that boosted it more, and she was using her magic to make herself grow and become human?