Some pictures would be helpfull, but here's what I would do based on what you have told us so far.
Get some hard wood dowel and cut to slightly overlenght the depth of the neck joint.
Using a bench drill, re-drill the holes wider to accept the dowels.
glue and tap in the dowel pegs.
when dry, sand the dowels flush and paint, laquer, finish. (whatever)
Re-drill the much smaller holes to accept your original screws.
If possible, your new dowels need to be MUCH wider than the current holes. So if the holes are now, say 3mm, then the dowels should be around 10mm
you get the drift?
hope that helps.
PS: Do NOT, under any circumstances use filler. It isn't strong enough and over time, your neck will go wobbly.