Well you can use modulus to get the end of the numbers (they will be the remainder). So just exclude the rows with ids of [-1,10,1000000] and then compute the modulus of 1000000:
print df
Id
0 -1
1 10
2 1000000
3 1000003
4 1000005
5 1000007
6 1000009
7 1000011
keep = df.Id.isin([-1,10,1000000])
df.Id[~keep] = df.Id[~keep] % 1000000
print df
Id
0 -1
1 10
2 1000000
3 3
4 5
5 7
6 9
7 11
Edit: Here is a fully vectorized string slice version as an alternative (Like Alex' method but takes advantage of pandas' vectorized string methods):
keep = df.Id.isin([-1,10,1000000])
df.Id[~keep] = df.Id[~keep].astype(str).str[1:].astype(int)
print df
Id
0 -1
1 10
2 1000000
3 3
4 5
5 7
6 9
7 11