I have never liked that people see national security and human rights (I am assuming here you mean Individual rights) as polar opposites.
The only reason why we should have national security is to defend individual rights. In this frame of thought, they are both tools to arriving at the same end, namely the protection of individual liberty.
So, to reply more directly, the actions taken by ANY government in order to repress individual rights is AGAINST national security. Why? Well, lets look at Mr. Bush. He has repeatedly abused individual rights for reasons he justified as being in the interest of national security. There are 2 main groups that he has oppressed, foreigners and domestics. With regard to the foreigners, removing their individual rights has only managed to create more enemies for America, and to harden their resolve. There is no inhumane treatment that will destroy the will of people to fight America. With regard to domestics, the continued oppression (wire tapping, etc.) and the silencing of descent has polarized the American political scene. The biggest threat to national security that this poses is that the people of America are (rightfully) skeptical and unwilling to follow the president on more "national security" ventures. While immediately this is ok, suppose war (or other military action) with another nation were necessary (like Iran or Saudi Arabia). People will be less willing to support it, and thus it may never be done correctly. Another example of this may be Iraq. By misleading the public and killing hundreds of thousands of innocent Iraqis the government has destroyed support for maintaining the occupation of Baghdad, even though (and admittedly it is Bush's own fault) it may be in the best interests of American national security for them to stay the course (though not prior to invading, and recent events in Iraq should make people optimistic of the Iraqis ability to self govern responsibly).