Step 1: Understanding the Concept
The Miyawaki method, developed by the Japanese botanist Akira Miyawaki, grows dense native mini-forests by planting many local species close together.
Step 2: In Maharashtra
Pilot plantations on this pattern in several districts are run by the State Forest Department together with another department.
Step 3: Conclusion
That partner is the Social Forestry Department.
Final Answer:
The partner agency is the Social Forestry Department.
\[ \boxed{\text{(C) }\text{Social Forestry Department}} \]