diff --git a/inst/tests/tests.Rraw b/inst/tests/tests.Rraw
index d7ffc476bb..fc52054d6c 100644
--- a/inst/tests/tests.Rraw
+++ b/inst/tests/tests.Rraw
@@ -3359,13 +3359,13 @@ Sep,33.5,19.4,15.7,11.9,0,100.8,100.8,0,12.7,12.7,0,174.1")
   test(1037.401, dim(ans<-melt(x, measure.vars=patterns("^y", "^z"))), INT(4,5))
   test(1037.402, ans$variable, factor(c("1","1","2","2")))
   test(1037.403, dim(ans<-melt(x, measure.vars=patterns("^y", "^z"), variable.factor=FALSE)), INT(4,5))
-  test(1037.404, ans$variable, c("1","1","2","2"))
+  test(1037.404, ans$variable, INT(1,1,2,2))
   x[, c("y1","z1"):=NA]
   test(1037.405, dim(melt(x, measure.vars=patterns("^y", "^z"))), INT(4,5))
   test(1037.406, dim(ans<-melt(x, measure.vars=patterns("^y", "^z"), na.rm=TRUE)), INT(2,5))
   test(1037.407, ans$variable, factor(c("2","2"), c("1", "2")))
   test(1037.408, dim(ans<-melt(x, measure.vars=patterns("^y", "^z"), na.rm=TRUE, variable.factor=FALSE)), INT(2,5))
-  test(1037.409, ans$variable, c("2","2"))
+  test(1037.409, ans$variable, INT(2,2))
 
   test(1037.410, melt(data.table(NULL), verbose=TRUE), data.table(NULL),
        output="ncol(data) is 0. Nothing to melt")
@@ -17417,13 +17417,13 @@ exid = data.table(id=1, expected)
 test(2182.3, melt(DTid, measure.vars=list(a=c(NA,1), b=2:3), id.vars="id"), exid)
 test(2182.4, melt(DTid, measure.vars=list(a=c(NA,"a2"), b=c("b1","b2")), id.vars="id"), exid)
 test(2182.5, melt(DT.wide, measure.vars=list(a=c(NA,1), b=2:3), na.rm=TRUE), data.table(variable=factor(2), a=2, b=2))
-test(2182.6, melt(DT.wide, measure.vars=list(b=c("b1","b2"))), data.table(a2=2, variable=factor(c("b1","b2")), b=c(1,2)), warning="measure.vars is a list with length=1") # measure.vars named list length=1, #5065
-# consistency between measure.vars=list with length=1 and length>1, #5209
-test(2182.71, melt(DT.wide, measure.vars=list("a2"), variable.factor=TRUE), data.table(b1=1, b2=2, variable=factor("a2"), value=2), warning="measure.vars is a list with length=1")
+test(2182.6, melt(DT.wide, measure.vars=list(b=c("b1","b2"))), data.table(a2=2, variable=factor(c("1","2")), b=c(1,2))) # list yields indices
+# consistency between measure.vars=list with length=1 and length>1 now uses indices for list case, #5209
+test(2182.71, melt(DT.wide, measure.vars=list("a2"), variable.factor=TRUE), data.table(b1=1, b2=2, variable=factor(1), value=2))
 test(2182.72, melt(DT.wide, measure.vars=c("a2"), variable.factor=TRUE), data.table(b1=1, b2=2, variable=factor("a2"), value=2))
-test(2182.73, melt(DT.wide, measure.vars=list("a2"), variable.factor=FALSE), data.table(b1=1, b2=2, variable="a2", value=2), warning="measure.vars is a list with length=1")
+test(2182.73, melt(DT.wide, measure.vars=list("a2"), variable.factor=FALSE), data.table(b1=1, b2=2, variable=1L, value=2))
 test(2182.74, melt(DT.wide, measure.vars=c("a2"), variable.factor=FALSE), data.table(b1=1, b2=2, variable="a2", value=2))
-test(2182.75, melt(data.table(a=10, b=20), measure.vars=list(n="a"), variable.factor=FALSE), data.table(b=20, variable="a", n=10), warning="measure.vars is a list with length=1")#thanks @mnazarov
+test(2182.75, melt(data.table(a=10, b=20), measure.vars=list(n="a"), variable.factor=FALSE), data.table(b=20, variable=1L, n=10))#thanks @mnazarov
 
 ### First block testing measurev
 # new variable_table attribute for measure.vars, PR#4731 for multiple issues
diff --git a/src/fmelt.c b/src/fmelt.c
index 54ad7b4de9..d00ad4a297 100644
--- a/src/fmelt.c
+++ b/src/fmelt.c
@@ -598,31 +598,42 @@ SEXP getvarcols(SEXP DT, SEXP dtnames, Rboolean varfactor, Rboolean verbose, str
   if (data->lvalues==1 && length(VECTOR_ELT(data->valuecols, 0)) != data->lmax)
     internal_error(__func__, "getvarcols %d %d", length(VECTOR_ELT(data->valuecols, 0)), data->lmax);  // # nocov
   if (isNull(data->variable_table)) {
-    if ((data->lvalues == 1) & data->measure_is_list) {
-      warning(_("measure.vars is a list with length=1, which as long documented should return integer indices in the 'variable' column, but currently returns character column names. To increase consistency in the next release, we plan to change 'variable' to integer, so users who were relying on this behavior should change measure.vars=list('col_name') (output variable is column name now, but will become column index/integer) to measure.vars='col_name' (variable is column name before and after the planned change)."));
-    }
     if (!varfactor) {
-      SET_VECTOR_ELT(ansvars, 0, target=allocVector(STRSXP, data->totlen));
-      if (data->lvalues == 1) {//one value column to output. TODO #5247 change to !data->measure_is_list
+      if (data->measure_is_list) {
+        // Return integer indices for list measure.vars (consistency with docs)
+        SET_VECTOR_ELT(ansvars, 0, target=allocVector(INTSXP, data->totlen));
+        int *td = INTEGER(target);
+        for (int j=0, ansloc=0; j<data->lmax; ++j) {
+          const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
+          for (int k=0; k<thislen; ++k) td[ansloc++] = j+1;
+        }
+      } else {
+        // same behavior for vector measure.vars: variable is column names
+        SET_VECTOR_ELT(ansvars, 0, target=allocVector(STRSXP, data->totlen));
         const int *thisvaluecols = INTEGER(VECTOR_ELT(data->valuecols, 0));
         for (int j=0, ansloc=0; j<data->lmax; ++j) {
           const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
           SEXP str = STRING_ELT(dtnames, thisvaluecols[j]-1);
           for (int k=0; k<thislen; ++k) SET_STRING_ELT(target, ansloc++, str);
         }
-      } else {//multiple value columns to output.
-        for (int j=0, ansloc=0, level=1; j<data->lmax; ++j) {
-          const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
-          char buff[20];
-          snprintf(buff, sizeof(buff), "%d", level++); // # notranslate
-          for (int k=0; k<thislen; ++k) SET_STRING_ELT(target, ansloc++, mkChar(buff));
-        }
       }
     } else {// varfactor==TRUE
       SET_VECTOR_ELT(ansvars, 0, target=allocVector(INTSXP, data->totlen));
       SEXP levels;
       int *td = INTEGER(target);
-      if (data->lvalues == 1) {//one value column to output. TODO #5247 change to !data->measure_is_list
+      if (data->measure_is_list) {
+        int nlevel = data->lmax;
+        levels = PROTECT(allocVector(STRSXP, nlevel)); protecti++;
+        for (int j=0; j<nlevel; ++j) {
+          char buff[20];
+          snprintf(buff, sizeof(buff), "%d", j+1); // # notranslate
+          SET_STRING_ELT(levels, j, mkChar(buff));
+        }
+        for (int j=0, ansloc=0; j<data->lmax; ++j) {
+          const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
+          for (int k=0; k<thislen; ++k) td[ansloc++] = j+1;
+        }
+      } else { // non-list measure.vars keeps legacy name-based levels
         SEXP thisvaluecols = VECTOR_ELT(data->valuecols, 0);
         int len = length(thisvaluecols);
         levels = PROTECT(allocVector(STRSXP, len)); protecti++;
@@ -645,16 +656,6 @@ SEXP getvarcols(SEXP DT, SEXP dtnames, Rboolean varfactor, Rboolean verbose, str
           const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
           for (int k=0; k<thislen; ++k) td[ansloc++] = md[j];
         }
-      } else {//multiple output columns.
-        int nlevel=0;
-        levels = PROTECT(allocVector(STRSXP, data->lmax)); protecti++;
-        for (int j=0, ansloc=0; j<data->lmax; ++j) {
-          const int thislen = data->narm ? length(VECTOR_ELT(data->not_NA_indices, j)) : data->nrow;
-          char buff[20];
-          snprintf(buff, sizeof(buff), "%d", nlevel + 1); // # notranslate
-          SET_STRING_ELT(levels, nlevel++, mkChar(buff));  // generate levels = 1:nlevels
-          for (int k=0; k<thislen; ++k) td[ansloc++] = nlevel;
-        }
       }
       setAttrib(target, R_LevelsSymbol, levels);
       setAttrib(target, R_ClassSymbol, ScalarString(char_factor));