RTA's toll free number to lodge a complaint/ make suggestion about auto rick/ taxi/ bus in Pune: 1800-2330012.
If you want to make a complaint in writing: Download RTA's Complaint form. RTA says that your name will not be disclosed.
Also for rickshaws:
1) Traffic Police Control Room: Call (24 hrs) 26123520. Road Transport Authority: Call (10 am - 5:45 pm) 26051414, 27492828. Fax (24 hrs): 26058282.
2) By SMS: Send the following SMS to 59994. Please note the spaces between the terms below.
rtopune rick-number complaint location date time
Here "complaint" should be very short, like demand excess fare/ refuse to ply/ arrogant behaviour etc.