Read a sci-fi novel years ago,
Are you sure it was a novel? It sounds a lot like "Goddess in Granite", a novelette by Robert F. Young (first published in The Magazine of Fantasy and Science Fiction, September 1957, available at the Internet Archive).
set on an alien planet
Marten found himself thinking of her sculptors, and for the thousandth time he speculated as to why they had sculptured her. In many ways, the problem resembled such Earth enigmas as the Egyptian pyramids, the Sacsahuaman Fortress, and the Baalbek Temple of the Sun. For one thing, it was just as irresolvable, and probably always would be, for the ancient race that had once inhabited Alpha Virginis IX had either died out centuries ago, or had migrated to the stars. In either case, they had left no written records behind them.
(Alpha Virginis = Spica is not really a likely location for an Earth-like planet.)
that featured a giant statue of a naked human woman lying on the ground.
She lay upon her back, her blue lakes of eyes gazing eternally upward. From his vantage point on her forearm, Marten had a good view of the mountains of her breasts. He looked at them contemplatively. They towered perhaps 8,000 feet above the chest-plateau, but, since the plateau itself was a good 10,000 feet above sea level, their true height exceeded 18,000 feet. However, Marten wasn't discouraged. It wasn't the mountains that he wanted.
If I remember, the statue was hundreds if not thousands of kilometers long.
In this story it's not that big:
The southern reaches of the shoulder-slope were less eroded than the central and northern reaches, and Marten edged closer and closer to the south rim. He had a splendid view of the Virgin's left side, and he stared, fascinated, at the magnificent, purple-shadowed escarpment stretching away to the horizon. Five miles from its juncture with the shoulder-slope, it dwindled abruptly to form her waist; three miles farther on, it burgeoned out to form her left hip; then, just before it faded into the lavender distances, it blended into the gigantic curve of her thigh.
Possibly her belly button was a lake.
No mention of her belly button, but her eyes are lakes:
She had begun as a natural phenomenon—an enormous geological upheaval—and actually all her sculptors had done, herculean though their labor had undoubtedly been, was to add the finishing touches and install the automatic subterranean pumping system that, for centuries, had supplied her artificial lakes of eyes with water from the sea.
Seem to remember the story started with the protagonist hiking on the statue.
Yep. The opening paragraph:
When he reached the upper ridge of the forearm, Marten stopped to rest. The climb had not winded him but the chin was still miles away, and he wanted to conserve as much of his strength as possible for the final ascent to the face.
Only other thing I can remember is the protagonist had 11 fingers.
FAIL. Nothing like that in the story.