خصم تكاليف استخراج التأشيرة عند الاستقالة بعد الخدمة أكثر من عام

That is specifically and explicitly not allowed.

You should make a complaint to the labor authority under which you were employed.

If you were employed on a Freezone visa, you need to contact the labor dispute section in that Freezone.

If you were employed on the mainland, you need to contact the Ministry of labor (you can call 800 60 to do so).