We performed a deep search for Herbig-Haro (HH) objects toward the Lupus I and III clouds, covering a sky area of ~ 1 and ~ 0.5 deg², respectively. In total, 11 new HH objects, HH 981--991, are discovered. The HH objects both in Lupus I and in Lupus III tend to be concentrated in small areas. The HH objects detected in Lupus I are located in a region of radius 0.26 pc near the young star Sz 68. The abundance of HH objects shows that this region of the cloud is active in on-going star formation. HH objects in the Lup III cloud are concentrated in the central part of the cloud around the Herbig Ae/Be stars HR 5999 and 6000. HH 981 and 982 in Lupus I are probably driven by the young brown dwarf SSTc2d J154457.9–342340 which has a mass of 50 M_J . HH 990 and 991 in Lup III align well with the HH 600 jet emanating from the low-mass star Par-Lup3-4, and are probably excited by this low-mass star of spectral type M5. High proper motions for HH 228 W, E, and E2 are measured, which confirms that they are excited by the young star Th 28. In contrast, HH 78 exhibits no measurable proper motion in the time span of 18 years, indicating that HH 78 is unlikely part of the HH 228 flow. The HH objects in Lup I and III are generally weak in terms of brightness and dimension in comparison to HH objects we detected with the same technique in the R CrA and Cha I clouds. Through a comparison with the survey results from the Spitzer c2d program, we find that our optical survey is more sensitive, in terms of detection rate, than the Spitzer IRAC survey to high-velocity outflows in the Lup I and III clouds.