The following bash script will automate the configuration of ntp to run in a jail (chroot) for a debian/ubuntu.

#!/bin/bash

/etc/init.d/ntp stop

rootfs=/var/chroot/ntp
mkdir -p $rootfs/{etc,var/lib/ntp,var/log}

mv /etc/ntp.conf $rootfs/etc
ln -s $rootfs/etc/ntp.conf /etc/ntp.conf

if [ -e /var/lib/ntp/ntp.drift ]; then
    mv /var/lib/ntp/ntp.drift $rootfs/var/lib/ntp
fi
ln -s $rootfs/var/lib/ntp/ntp.drift \
    /var/lib/ntp/ntp.drift
chown -R ntp:ntp $rootfs/var/lib/ntp

mv /var/log/ntpstats $rootfs/var/log
ln -s $rootfs/var/log/ntpstats /var/log/ntpstats
chown -R ntp:ntp $rootfs/var/log/ntpstats

sed -e "s,'-g','-4 -i /var/chroot/ntp -g'," \
    /etc/default/ntp > /tmp/x && \
    mv /tmp/x /etc/default/ntp

sed -e "s,restrict -6,#restrict -6," \
    -e "s,restrict ::1,#restrict ::1," \
    /etc/ntp.conf > /tmp/x && \
    mv /tmp/x /etc/ntp.conf

/etc/init.d/ntp start

To check if the chroot is well configured, you can execute this command :

# ps -ef | grep ntp
ntp        696     1  0 08:52 ?        00:00:00 /usr/sbin/ntpd -p /var/run/ntpd.pid -4 -i /var/chroot/ntp -g -u 110:119

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Reference

Source

Script source

Access Control Commands and Options

• discard – specify headway parameters
• restrict – specify access restrictions
• Command Index

Authentication Commands and Options

• automax – specify Autokey regeneration interval
• controlkey – specify control key ID
• crypto – configure Autokey parameters
• ident – specify Autokey ephemeral group name
• keys – specify symmetric keys filename
• keysdir – specify Autokey key directory
• requestkey – specify request key ID
• revoke – specify Autokey randomization interval
• trustedkey – specify trusted key IDs
• Command Index

Server Commands and Options

• server – configure client association
• peer – configure symmetric peer association
• broadcast – configure broadcast server association
• manycastclient – configure manycast client association
• pool – configure pool association
• unpeer – remove association
• broadcastclient – enable broadcast client
• manycastserver – enable manycast server
• multicastclient – enable multicast client
• Command Index

Monitoring Commands and Options

• filegen – specify monitor files
• statistics – enable writing of statistics records
• statsdir – specify monitor files directory
• Command Index

Reference Clock Commands and Options

• fudge – specify fudge parameters
• server – specify reference clock server
• Command Index

Miscellaneous Commands and Options

• broadcastdelay – specify broadcast delay
• driftfile – specify frequency file
• enable – enable options
• disable – disable options
• includefile – specify include file
• interface – specify which local network addresses to use
• leapfile – specify leapseconds file
• logconfig – configure log file
• mru – control monitor MRU list limits
• phone – specify modem phone numbers
• reset – reset groups of counters
• saveconfigdir – specify saveconfig directory
• setvar – set system variables
• tinker – modify sacred system parameters (dangerous)
• rlimit – alters certain process storage allocation limits
• tos – modify service parameters
• trap – set trap address
• ttl – set time to live
• Command Index