Officials at the Erez crossing point between Israel and the coastal territory discovered the explosives hidden in tubes of "medical material", it said, without giving further details.
"It is believed that they were to be used in Hamas terrorist attacks in the near future," it said, referring to the Islamist movement that runs the Gaza Strip.
One of the sisters was heading for cancer treatment in Israel, while the other was accompanying her, it added.
It said the two were arrested and an investigation was ongoing.
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