diff --git a/tools/external_ic.F90 b/tools/external_ic.F90
index f3611b867..616175c8d 100644
--- a/tools/external_ic.F90
+++ b/tools/external_ic.F90
@@ -3084,6 +3084,7 @@ subroutine remap_scalar(Atm, km, npz, ncnst, ak0, bk0, psc, qa, zh, omga, t_in)
 
 ! map tracers
       do iq=1,ncnst
+        if (floor(qa(is,j,1,iq)) == -1000) cycle !skip missing scalars [floor(-999.99) is -1000]
          do k=1,km
             do i=is,ie
                qp(i,k) = qa(i,j,k,iq)