Put the certificates to the /etc/pki as suggested by:
http://fedoraproject.org/wiki/PackagingDrafts/Certificates
diff -ru openvas-scanner-4.0.1/CMakeLists.txt openvas-scanner-4.0.1.pki/CMakeLists.txt
--- openvas-scanner-4.0.1/CMakeLists.txt	2014-04-23 16:00:47.000000000 +0200
+++ openvas-scanner-4.0.1.pki/CMakeLists.txt	2014-05-26 15:48:26.184941485 +0200
@@ -157,15 +157,16 @@
 set (OPENVAS_CACHE_DIR   "${LOCALSTATEDIR}/cache/openvas")
 set (OPENVAS_PID_DIR     "${LOCALSTATEDIR}/run")
 set (OPENVAS_SYSCONF_DIR "${SYSCONFDIR}/openvas")
+set (OPENVAS_CERT_DIR    "${SYSCONFDIR}/pki/openvas")
 
 set (OPENVAS_NVT_DIR     "${OPENVAS_STATE_DIR}/plugins")
 
 set (OPENVAS_LIB_INSTALL_DIR     "${LIBDIR}")
-set (OPENVAS_SCANNER_CERTIFICATE "${OPENVAS_STATE_DIR}/CA/servercert.pem")
-set (OPENVAS_SCANNER_KEY         "${OPENVAS_STATE_DIR}/private/CA/serverkey.pem")
-set (OPENVAS_CLIENT_CERTIFICATE  "${OPENVAS_STATE_DIR}/CA/clientcert.pem")
-set (OPENVAS_CLIENT_KEY          "${OPENVAS_STATE_DIR}/private/CA/clientkey.pem")
-set (OPENVAS_CA_CERTIFICATE      "${OPENVAS_STATE_DIR}/CA/cacert.pem")
+set (OPENVAS_SCANNER_CERTIFICATE "${OPENVAS_CERT_DIR}/CA/servercert.pem")
+set (OPENVAS_SCANNER_KEY         "${OPENVAS_CERT_DIR}/private/CA/serverkey.pem")
+set (OPENVAS_CLIENT_CERTIFICATE  "${OPENVAS_CERT_DIR}/CA/clientcert.pem")
+set (OPENVAS_CLIENT_KEY          "${OPENVAS_CERT_DIR}/private/CA/clientkey.pem")
+set (OPENVAS_CA_CERTIFICATE      "${OPENVAS_CERT_DIR}/CA/cacert.pem")
 
 set (OPENVASSD_MESSAGES "${OPENVAS_LOG_DIR}/openvassd.messages")
 set (OPENVASSD_DEBUGMSG "${OPENVAS_LOG_DIR}/openvassd.dump")
diff -ru openvas-scanner-4.0.1/tools/openvas-mkcert-client.in openvas-scanner-4.0.1.pki/tools/openvas-mkcert-client.in
--- openvas-scanner-4.0.1/tools/openvas-mkcert-client.in	2014-01-21 12:26:20.000000000 +0100
+++ openvas-scanner-4.0.1.pki/tools/openvas-mkcert-client.in	2014-05-26 15:49:28.089433621 +0200
@@ -26,8 +26,8 @@
 
 umask 022
 
-OPENVASPRIV="@OPENVAS_STATE_DIR@/private/CA"
-OPENVASPUB="@OPENVAS_STATE_DIR@/CA"
+OPENVASPRIV="@OPENVAS_CERT_DIR@/private/CA"
+OPENVASPUB="@OPENVAS_CERT_DIR@/CA"
 
 usage()
 {
diff -ru openvas-scanner-4.0.1/tools/openvas-mkcert.in openvas-scanner-4.0.1.pki/tools/openvas-mkcert.in
--- openvas-scanner-4.0.1/tools/openvas-mkcert.in	2014-01-21 12:26:20.000000000 +0100
+++ openvas-scanner-4.0.1.pki/tools/openvas-mkcert.in	2014-05-26 15:51:35.264444646 +0200
@@ -44,8 +44,8 @@
 datadir=@DATADIR@
 bindir=@BINDIR@
 sbindir=@SBINDIR@
-OPENVASPRIV="@OPENVAS_STATE_DIR@/private/CA"
-OPENVASPUB="@OPENVAS_STATE_DIR@/CA"
+OPENVASPRIV="@OPENVAS_CERT_DIR@/private/CA"
+OPENVASPUB="@OPENVAS_CERT_DIR@/CA"
 
 BASEDIR=${TMPDIR-/tmp}/openvas-mkcert.$$