Code:
awk -F, '
($4 == 888 || $4 == 0) && !($3 == 55 || $3 == 16 || $3 == 76) {print "DEPT ", $3, $4, $0; next}
{print "CLASS", $3, $4, $0}
' OFS="\t" file
DEPT 43 888 290,1663,43,888,0,0.00,86.91,0.00,26.98,0.00
DEPT 52 0 290,1663,52,0,0,0.00,0.00,0.00,0.00,0.00
DEPT 52 888 290,1663,52,888,0,0.00,34.60,0.00,9.00,0.00
CLASS 76 5 290,1663,76,5,0,0.00,86.91,0.00,26.98,0.00
CLASS 52 2 290,1663,52,2,0,0.00,0.00,0.00,0.00,0.00
CLASS 52 999 290,1663,52,999,0,0.00,34.60,0.00,9.00,0.00
CLASS 16 705 290,1663,16,705,0,0.00,34.60,0.00,9.00,0.00
CLASS 76 888 290,1663,76,888,0,0.00,86.91,0.00,26.98,0.00
CLASS 55 0 290,1663,55,0,0,0.00,0.00,0.00,0.00,0.00
DEPT 52 888 290,1663,52,888,0,0.00,34.60,0.00,9.00,0.00
CLASS 16 888 290,1663,16,888,0,0.00,34.60,0.00,9.00,0.00
DEPT 1 888 290,1663,1,888,0,0.00,34.60,0.00,9.00,0.00