An email by Mr Stoner's office, obtained in a call for papers by the Greens, instructs the Department of Regional Infrastructure and Services to send a letter to the Planning Minister, Brad Hazzard, outlining the benefits of Shenhua's proposal.
The project is described as "State significant" and should be given the go-ahead "as quickly as possible".
NSW Farmers' Association mining taskforce chair, Fiona Simson, said the documents raise questions about the Namoi Water Study, designed to assess the impact of mining on agriculture in the region.
The email stated the approval process "should not be held up by" the study.
"We are extremely concerned about the information and we are seeking information from the government about the process," Ms Simson said.
"The reason why we supported this process was because it looked at the whole catchment.
"The government is going back to the previous government's policy and we are seeking clarification from it on its policy."
About 1000 documents outlining exchanges between Shenhua, its consultants and the Coalition, have been tabled in the NSW Parliament.