The phrase ag+VN is continuous present, or progressive present, it's adding the "ing" as we do in English. I think they are trying to convey this usage: ag obair = working, ag ithe = eating, ag rith = running, etc... "The secretary is not at work" conveys the same message but it's not the same translation.
Sorry if this is a stupid question, but is it "níl" here instead of "ní" because of the "ag" in "ag obair?" If so, I believe there was a phrase from many lessons ago which was along the lines of: "Tá sí ag féachaint ar an mbuachaill." So would the negative form of that be: "Níl sí ag féachaint ar an mbuachaill?"