Q:

When does Batman first fight the Suicide Squad in the comics?

It's been hinted that Batman features in the upcoming Suicide Squad movie. 
These is plausible to me but it seems odd that he would be directly opposed to a squad of anti-heroes. 
When in the comics do they first fight? 

A:

Batman first starts to investigate them in Suicide Squad #10 "Up Against the Wall" in which Batman confronts Amanda Waller about the Suicide Squad, and Batman acquiesces to wait for another day to take the group down. 

Batman infiltrated Belle Reve to confirm if the Suicide Squad is real. After confronting Amanda Waller, telling her that he will blow the whistle on the covert government team, Batman seems like he has the upper hand. However, Amanda Waller informs Batman that she will use all of her extensive resources to find out who Batman really is and report that to the media as well. Feeling stymied, Batman reluctantly agrees to keep the Suicide Squad a secret until he can find another way to take them down.

