diff --git a/distribution/src/main/resources/bin/elasticsearch-env b/distribution/src/main/resources/bin/elasticsearch-env
index 211c872b9a5..e4be2625217 100644
--- a/distribution/src/main/resources/bin/elasticsearch-env
+++ b/distribution/src/main/resources/bin/elasticsearch-env
@@ -45,8 +45,7 @@ if [ ! -x "$JAVA" ]; then
   exit 1
 fi
 
-# don't let JAVA_TOOL_OPTIONS slip in (e.g. agents in Ubuntu); works around
-# https://bugs.launchpad.net/ubuntu/+source/jayatana/+bug/1441487
+# do not let JAVA_TOOL_OPTIONS slip in (as the JVM does by default)
 if [ "x$JAVA_TOOL_OPTIONS" != "x" ]; then
   echo "warning: ignoring JAVA_TOOL_OPTIONS=$JAVA_TOOL_OPTIONS"
   unset JAVA_TOOL_OPTIONS
diff --git a/distribution/src/main/resources/bin/elasticsearch-env.bat b/distribution/src/main/resources/bin/elasticsearch-env.bat
index c1d6f43b15c..69bd697d28b 100644
--- a/distribution/src/main/resources/bin/elasticsearch-env.bat
+++ b/distribution/src/main/resources/bin/elasticsearch-env.bat
@@ -28,6 +28,12 @@ if not exist %JAVA% (
   exit /b 1
 )
 
+rem do not let JAVA_TOOL_OPTIONS slip in (as the JVM does by default)
+if not "%JAVA_TOOL_OPTIONS%" == "" (
+  echo "warning: ignoring JAVA_TOOL_OPTIONS=$JAVA_TOOL_OPTIONS"
+  set JAVA_TOOL_OPTIONS=
+)
+
 rem JAVA_OPTS is not a built-in JVM mechanism but some people think it is so we
 rem warn them that we are not observing the value of %JAVA_OPTS%
 if not "%JAVA_OPTS%" == "" (
diff --git a/docs/reference/setup/sysconfig/configuring.asciidoc b/docs/reference/setup/sysconfig/configuring.asciidoc
index 7ec9e1d405d..0473bed3a76 100644
--- a/docs/reference/setup/sysconfig/configuring.asciidoc
+++ b/docs/reference/setup/sysconfig/configuring.asciidoc
@@ -125,3 +125,16 @@ export ES_JAVA_OPTS="$ES_JAVA_OPTS -Djava.io.tmpdir=/path/to/temp/dir"
 
 When using the RPM or Debian packages, `ES_JAVA_OPTS` can be specified in the
 <<sysconfig,system configuration file>>.
+
+The JVM has a built-in mechanism for observing the `JAVA_TOOL_OPTIONS`
+environment variable. We intentionally ignore this environment variable in our
+packaging scripts. The primary reason for this is that on some OS (e.g., Ubuntu)
+there are agents installed by default via this environment variable that we do
+not want interfering with Elasticsearch.
+
+Additionally, some other Java programs support the `JAVA_OPTS` environment
+variable. This is *not* a mechanism built into the JVM but instead a convention
+in the ecosystem. However, we do not support this environment variable, instead
+supporting setting JVM options via the `jvm.options` file or the environment
+variable `ES_JAVA_OPTS` as above.
+