It’s quite easy. If you check keytool manual you can see the following:
$ keytool -importcert -help
keytool -importcert [OPTION]...
Imports a certificate or a certificate chain
Options:
... removed for clearity
-cacerts access the cacerts keystore
To get rid of that warning you must use -cacerts option instead of calling cacert keystore:
keytool -import -trustcacerts -cacerts -storepass changeit -noprompt -alias my_root_ca.pem -file /usr/share/ca-certificates/foo/my_root_ca.pem