A more recent (and canonical) answer comes from 2016's Star Wars: Complete Locations. It's a compilation of a lot of previously published material, including the images and text in the other answer here. However, there's a bit of extra information on page 16:
Naboo is a bizarre, geographically (sic) unique world located along a major galactic trade route near the Outer Rim. The planet's serene surface of sweeping hills and rolling seas is deceptive: beneath it lies a shadowy underwater world of winding caverns and tunnels inhabited by gigantic, ferocious sea creatures. This immense labyrinth runs through the entire planet, becoming increasingly rocky and dense in the lower strata. The planet's center seethes and bubbles with eruptions of exotic plasmic energy. Over millennia these eruptions form new caverns and tunnels, and influence surface features such as mountains. The planet's two primary civilisations, the Naboo and the Gungans, rely on this plasma power, although they collect and use it in different ways.
I suspect "geographically unique" was meant to be "geologically unique".
This does seem to say that the centre of the planet consists of plasma, not magma. Why that may be is not stated directly, but later in the book while discussing the power station of Theed (where Obi-Wan and Qui-Gon fought Maul), we do get this mention on page 55:
Mining Plasma: Deep within Naboo, plasma is constantly generated by natural ionization reactions.
Pretty vague. However, there's another nugget that seems rather intriguing, back on page 18:
The diverse terrain of Naboo teems with luscious plant and animal life. Whether it's the rich, green plains and insect-ridden swamps of the surface or the dark, fish-rich depths of the oceans, Naboo offers fruitful existences to those inhabitants who live in harmony with the planet. Several Gungan and Naboo chroniclers have advanced the theory that the mysterious and now long-dead civilisation whose ruins dot the countryside failed to respect this balance and were destroyed by their greed.
Now, Speculation alert! this suggests to me that the mysterious civilisation in question may have deliberately engineered the planet's core to produce plasma, and that engineering was what destroyed them. It's certainly not explicit, but it would explain the unique strangeness of Naboo.