Posting my findings with the hope that it would be of help to someone out there.

system and backtick both fork a child process. Backtick differs from system in that it opens a pipe for gathering the child process/command’s output. And this is what perl doc on fork has to say about file descriptors:

Any filehandles open at the time of the fork() will be dup()-ed. Thus, the files can be closed independently in the parent and child, but beware that the dup()-ed handles will still share the same seek pointer. Changing the seek position in the parent will change it in the child and vice-versa. One can avoid this by opening files that need distinct seek pointers separately in the child. On some operating systems, notably Solaris and Unixware, calling exit() from a child process will flush and close open filehandles in the parent, thereby corrupting the filehandles. On these systems, calling_exit() is suggested instead. _exit() is available in Perl through the POSIX module. Please consult your system's manpages for more information on this

So, whatever file descriptors/handles were open at the time of executing system/backtick are inherited by the child process/command. Which means processes like ntpd/dhcpd/named etc inherit all of the parent perl process' open file descriptors including any pipes opened as part of backtick.

Somehow ntpd, in my case, also inherited the write-end of the pipe which is the reason the parent process, which had the read-end of the pipe, was stuck in read(2) indefinitely because ntpd is a long running process. Now, the parent process closes the write-end of the pipe before forking but the whole operation of opening the pipe and closing the write-end is not atomic so .......

perl process

backtick

pipe()

<---------- GAP HERE

close() write-end of pipe

The solution I used was to write a perl wrapper script which closes all fds except 0/1/2 and then exec the command, like this:

`closed.pl service xyz restart`;

There are multiple ways of closing fds. I used the tips from the following discussion : http://www.perlmonks.org/?node_id=476086

Here's a link which describes a similar issue : http://tdistler.com/2010/06/18/stop-stealing-my-file-descriptors