You can try this custom adapter to hide items from spinner based on position of item in spinner.
public class CustomAdapter extends ArrayAdapter<String> {
     private int hidingItemIndex;
     public CustomAdapter(Context context, int textViewResourceId, String[] objects, int hidingItemIndex) {
         super(context, textViewResourceId, objects);
         this.hidingItemIndex = hidingItemIndex;
     }
     @Override
     public View getDropDownView(int position, View convertView, ViewGroup parent) {
         View v = null;
         if (position == hidingItemIndex) {
             TextView tv = new TextView(getContext());
             tv.setVisibility(View.GONE);
             v = tv;
         } else {
             v = super.getDropDownView(position, null, parent);
         }
         return v;
     }
 }
check this link for reference How to hide one item in an Android Spinner
the other way would be removing item from array list and set to spinner.