There are a number of topics on the web, about getting a modified version of motion (motion-mmcal) to work with raspberry pi v2.1 CSI camera.

A simpler method is to expose the camera interface through the standard video 4 linux kernel interface /dev/video0.

This can be achieved by simply enabling the video 4 linux kernel module and installing the standard motion.

Install motion

Enable the kernel module on boot

Load the module without reboot

Start service as normal