Try this:
import importlib
module1 = importlib.import_module('module1.module')
module2 = importlib.import_module('module2.module')
That said, __import__
should work too. You just need to take out the "modules" at the beginning, like so (I've set up a similar directory structure to you):
In [3]: __import__('module1.module')
Out[3]: <module 'module1' from 'module1/__init__.py'>