--- a/src/utils/ncmpidiff/Makefile.am
+++ b/src/utils/ncmpidiff/Makefile.am
@@ -18,7 +18,7 @@
 cdfdiff_SOURCES = cdfdiff.c
 
 cdfdiff$(EXEEXT): cdfdiff.c Makefile
-	$(SEQ_CC) -I$(top_srcdir)/src/utils/ncvalidator -o $@ $<
+	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -I$(top_srcdir)/src/utils/ncvalidator -o $@ $<
 
 $(top_builddir)/src/libs/libpnetcdf.la:
 	set -e; cd $(top_builddir)/src/libs && $(MAKE) $(MFLAGS)
--- a/src/utils/ncoffsets/Makefile.am
+++ b/src/utils/ncoffsets/Makefile.am
@@ -10,7 +10,7 @@
 EXTRA_DIST = ncoffsets.c
 
 ncoffsets$(EXEEXT): ncoffsets.c
-	$(SEQ_CC) -o $@ $<
+	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -o $@ $<
 
 dist_man_MANS = ncoffsets.1
 
--- a/src/utils/ncvalidator/Makefile.am
+++ b/src/utils/ncvalidator/Makefile.am
@@ -76,7 +76,7 @@
 TST_HDF5_FILES = pad_superblock.h5
 
 ncvalidator$(EXEEXT): ncvalidator.c Makefile
-	$(SEQ_CC) -o $@ $<
+	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -o $@ $<
 
 # autimake 1.11.3 has not yet implemented AM_TESTS_ENVIRONMENT
 # For newer versions, we can use AM_TESTS_ENVIRONMENT instead
--- a/src/utils/pnetcdf_version/Makefile.am
+++ b/src/utils/pnetcdf_version/Makefile.am
@@ -22,7 +22,7 @@
 endif
 
 pnetcdf_version$(EXEEXT): pnetcdf_version.c
-	$(SEQ_CC) $(XDEFS) -o $@ $<
+	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE $(XDEFS) -o $@ $<
 
 dist_man_MANS = pnetcdf_version.1