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this is disgusting going on over . i have been going through same situation. i have worked in dunai almost 4 year and i got another job in Rasal khaima but when my new empoyer applied for my work permit it got rejected due to security reason not clearifying the reason. i have cleared record never involved any bad activity and never done anything wrong yet they have put me in big trouble by making my job lost. i am going back home and will never visit uae as if we go to process our visa again it will raise the same issue as it may have falsely  recorded in their system.

First of all, the rejection is never automatically done by the system. 

Then, the fact that you need to keep in mind is that rejections may have nothing to do with YOU as a person but rather, could be due to political elements related to your nationality, faith or affiliations.  Because at a Government level, they can decide, at any time, without notifying anyone, that we don't want people having x or y profile in the country anymore. 

I can give an unrelated example.  For Pakistan, if you were born in certain areas, you will never get a visit or work visa for the UAE.  Before this came into effect, there must have been people who made it to the UAE despite being from those areas.   The Government can decide to no longer renew the visas for those people at any time if they want and that will be classifed as a security rejection.   This is a simple example but things can be very complex and reasons not very clear.  And one fact that I keep telling people.........and they don't listen is:  They will NEVER tell you the reason for rejection so don't even bother trying.

I won't debate the right or wrong of this but just to make it simple, there is absolutely nothing you can do about it if you don't have a strong wasta (Connection with decision makers).