You can seek relief from pending high court matter after stating above facts on record 

Dear Client,

Your advocate can draft a cease and desist letter addressed to the local Muslim body and any other parties involved in the encroachment. This letter demands that they immediately stop their activities on the disputed land and vacate the premises. It also serves as documentation of your intent to protect your property rights. If the encroachment persists despite the cease and desist letter, you can file a case against the encroaching party in civil court. This case would seek remedies such as an injunction to stop the encroachment, damages for any harm caused to your property, and possibly eviction of the encroaching party.

As you have said that there is already case is going on in this regard, you may have to wait for the disposal.

This is a dispute between the land owner and the state government hence any opinion given to the matter which is subjudice, would be a misleading one. 

Owner should file police complaint t of criminal trespass against encroacher under section 447 of IPC 

2)file suit for eviction against encroacher 

- Since, the said matter is pending before the High Court, then any encroachment in the said land will be considered as an offence , even the encroacher is a pawn of government

- You can lodge a complaint before the police and higher official against that local body , and if no action then you can move an application before the same court in High Court for passing a restraining order...