Mark, the ntp profile in Ubuntu supports the NTPD_DEVICE tunable and
after reading https://www.kernel.org/doc/Documentation/pps/pps.txt it
seems like this would be the appropriate place to put this. Eg

$ cat /etc/apparmor.d/tunables/ntpd
...
#Add your ntpd devices here eg. if you have a DCF clock
# @{NTPD_DEVICE}="/dev/ttyS1"
@{NTPD_DEVICE}="/dev/null"

Adjust that to be:
@{NTPD_DEVICE}="/dev/pps[0-9]*"

Then do:
sudo apparmor_parser -r /etc/apparmor.d/usr.sbin.ntpd

The above expands to the equivalent line you proposed in the
description.

Would this suit your needs?

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Touch seeded packages, which is subscribed to ntp in Ubuntu.
https://bugs.launchpad.net/bugs/1564832

Title:
  Apparmor profile for NTPd needs to allow read/write access to
  /dev/ppsX

Status in ntp package in Ubuntu:
  Triaged

Bug description:
  Am trying to get NTP to work with the kernel PPS subsystem, for high-
  accuracy GPS-based clocks. On startup of NTPd I see this:

  Apr  1 11:18:58 doorway kernel: [  300.387443] audit: type=1400
  audit(1459505938.042:9): apparmor="DENIED" operation="open"
  profile="/usr/sbin/ntpd" name="/dev/pps0" pid=1668 comm="ntpd"
  requested_mask="wr" denied_mask="wr" fsuid=0 ouid=0

  Adding this to the usr.sbin.ntpd apparmor profile eliminated the
  error:

    /dev/pps[0-9]* rw,

  
  I'm not sure why ntpd needs *write* access to ppsN though, perhaps that can 
be improved.

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