A young NSA Agent impersonates a government minister at a secret meeting on the global arms trade to terrorists. But when masked gunmen storm the building, their target is not the minister he impersonates, but the NSA Agent himself.

Essentialy the under cover agent discovers that his agency is after him. That's your hook, but I don't think your logline is really expressing this dramatically enough. The whole first sentence can be cut, as it doesn't describe the main plot, all you need to write is:
After and under cover CIA agent on a mission is targeted by his fellow operatives he must?

The specifics of his initial mission are unimportant as the inciting incident is the CIA's attempt on his life. I changed it to CIA as they would likely be more inclined to undertake such operations.

Problem is you didn't describe the goal, after he realises?that they are after him what MUST he do? This is a crucial element of a logline and needs to be described.

Try and get this down to one sentence and simplify it, for example;

A young man infiltrates a secret arms trade between the US government and Middle-Eastern terrorists to stop it but the meeting is stormed by masked gunmen looking for him...

I think ink you need a little more. What?specifically?is your protagonist doing there? What is his flaw (what makes him sympathetic to the audience)? What do the terrorists want?

Hope this helps.

Try and get this down to one sentence and simplify it, for example;

A young man infiltrates a secret arms trade between the US government and Middle-Eastern terrorists to stop it but the meeting is stormed by masked gunmen looking for him...

I think ink you need a little more. What?specifically?is your protagonist doing there? What is his flaw (what makes him sympathetic to the audience)? What do the terrorists want?

Hope this helps.