I have the following type of arrays:
a = array([[1,1,1],
[1,1,1],
[1,1,1],
[2,2,2],
[2,2,2],
[2,2,2],
If you don't mind mapping to tuples just to get the count you can use a Counter dict which runs in 28.5 µs
on my machine using python3 which is well below your threshold:
In [5]: timeit Counter(map(tuple, a))
10000 loops, best of 3: 28.5 µs per loop
In [6]: c = Counter(map(tuple, a))
In [7]: c
Out[7]: Counter({(2, 2, 2): 3, (1, 1, 1): 3, (3, 3, 0): 3})