CAUTION!
Well, this is dependent on what you are shooting. In a lot of handguns, cartridges producing low velocities using fast powders are best for target shooting because what you describe is common. In rifles, using rifle powders, what you describe is actually dangerous. Dr. Lloyd Brownell showed decades ago that shooting rifle powders (his were mostly IMR 4198, 3031, 4895, and 4064 in a .30-06 at that time) at 40% case capacity would occasionally produce a measured 2X maximum pressure spike, well over proof load levels. He said the barrel of the gun they used in his tests (a nickel steel Springfield '03) had bulges in several places before they finished testing.
With rifle powders you should generally avoid loading below 70% fill of the space in the case under the bullet (70% load density), and never go below 60% unless the manufacturer states specifically that it is OK to do with a particular powder whose characteristics are unusual in this regard. Having seen Brownell's pressure plots, I won't do it even then and keep 60% as a hard limit.
At 40-50% loads, pressures are going to drop very roughly in proportion to an exponent of around 1.5 to 3, depending on the powder, so you are at 1/3 to 1/16 of normal operating pressure. With typical rifle powders, this is going to produce very dirty burn (lots of residue left behind) because slow powders burn very incompletely at such low pressures, so most of the powder is wasted. Switching to a bulky fast powder like Trail Boss is much better for such slow loads and will use much lighter charges that burn much more completely and cleanly and will save you money in dollars per foot per second at the muzzle.
If you are working with rifle loads, the accuracy you see will be at short ranges and is due simply to the recoil moments and pressures being too low to distort and whip the barrel around. Once you get beyond 200 yards, the large arc in the trajectory will make for a lot of vertical stringing because the low loads will product inconsistent muzzle velocities. Making higher pressure loads shoot accurately, particularly in a rifle with a light weight barrel contour requires tuning the loads to coordinate the moment of the bullet exit from the muzzle with a calm spot in the whipping cycle and in barrel distortion. I and another board member are starting to explore a new approach to this, but for now
Dan Newberry's OCW method seems to be the best one around. Once you get a bullet correctly synchronized with the muzzle, you should get good groups and have the velocity consistency and flat shooting that will let you shoot well for hundreds of yards.
Let us know what chambering, barrel length and bullet you are loading, and w can make recommendations for light loads for short range. For long ranges you will find you actually need more velocity.