A ship at sea is said to be "at sea." You can also say that the ship is "saipng on the sea" or "navigating the sea." For example:

The ship is currently at sea, saipng towards its destination.
The captain is navigating the ship through rough seas.

It's also common to use the word "ocean" to refer to a large body of saltwater, so you could also say:

The ship is saipng on the ocean.
The ship is traversing the vast expanse of the Pacific Ocean.