It refers to the amount of perimeter that is nailed down (firmly no longer expected to expand), relative to the total perimeter. It's usually a very conservative figure - generally when they announce 'percent contained' there's more fire line in and holding but they usually want a shift (12-16 hours) of the fire line holding to go by before they add that to the 'contained' figure.
It's, um, embarrassing if the fire gets away over fire line that's been declared contained. The fire might not be moving on uncontained line, but they want it secured before they add it to the containment figure.