Can I purchase Basic Economy flights with the contracted travel agency?

Yes. All fares, including basic economy, are eligible for purchase. 

When using Concur, a warning is provided to inform you that there are limitations with Basic Economy fares, including that there would be no refund in the event of cancellation.  If the fare meets your business need and you are willing to accept the risks, simply acknowledge that you understand the restrictions and continue with the purchase.  If you are an arranger and booking on behalf of a traveler, be sure they understand the restrictions that may impact their travel.