Cut the trees in the boundary

My land sharing one side with the irrigation department. i have some trees in the boundary. After new survey that trees came under irrigation department. After checking with old sketch, i found there have a wrong calculation in the new sketch. I reported this to survey department too. The survey department not solved the issue for past 1 year. When my parents spoke with the survey head, he told we can cut our trees no problem. Later 2 weeks before, a wood merchant cut those trees. After one week over irrigation department people came and gave a notice and signed acknowledgement. The notice says we have cut the trees of irrigation department, So have to present in the office within 3 days and put the cut trees back. Unless will be filed case. Then my parents visited the irrigation office with my uncle, the officer was busy with some minister visit, so he told to no time to discuss now. My parents are senior citizens, so he told no need to come again, he will discuss with my uncle. 4 days later my uncle visited the office, then he said a large amount as fine. if not paid, they will file the case in the court. Those trees not much valuable,used for cooking and heating. My questions are. 1. No one seen my parents cutting the trees, So how can they file a case against my parents ?. 2. They haven't seen my parents cutting the tree , or by someone. Without witness can a case filed ? 3. If my parents say, they haven't cut the trees and no witness for the action. What will be the next step ?