The Mulliken charges are output in *.out by default as shown in Section 'Test calculation'. In addition to the Mulliken charge projected to each atom, you can also find a decomposed Mulliken charge to each orbital in *.out. The output result stored in *.out for a methane molecule is as follows:
Decomposed Mulliken populations
1 C Up spin Down spin Sum Diff
multiple
s 0 0.598003833 0.598003833 1.196007667 0.000000000
sum over m 0.598003833 0.598003833 1.196007667 0.000000000
sum over m+mul 0.598003833 0.598003833 1.196007667 0.000000000
px 0 0.588514081 0.588514081 1.177028163 0.000000000
py 0 0.588703212 0.588703212 1.177406424 0.000000000
pz 0 0.588514081 0.588514081 1.177028162 0.000000000
sum over m 1.765731375 1.765731375 3.531462749 0.000000000
sum over m+mul 1.765731375 1.765731375 3.531462749 0.000000000
2 H Up spin Down spin Sum Diff
multiple
s 0 0.409066346 0.409066346 0.818132693 0.000000000
sum over m 0.409066346 0.409066346 0.818132693 0.000000000
sum over m+mul 0.409066346 0.409066346 0.818132693 0.000000000
3 H Up spin Down spin Sum Diff
multiple
s 0 0.409065912 0.409065912 0.818131824 0.000000000
sum over m 0.409065912 0.409065912 0.818131824 0.000000000
sum over m+mul 0.409065912 0.409065912 0.818131824 0.000000000
.......
....
As you can see, the Mulliken charges are decomposed for all orbitals.
There are two kind of summations in this decomposition.
One of summations is 'sum over m' which means a summation over
magnetic quantum number for each multiple orbital.
The second summation is 'sum over m+mul' which means a summation
over both magnetic quantum number and orbital multiplicity, where
"multiple" means a number to specify a radial wave function.
Therefore, Mulliken charges are decomposed to contributions of
all orbitals.