Resolution:
You can put the "shutdown" command into a script file and pass the script file to tibemsadmin command.

In the script file, you need to provide the server url to connect to specific server.

connect [server-url {admin|user_name} password]

The server url is in this format,
tcp://&ltIP_address_of_EMS_server>:&ltport>

For example, if EMS server is running on 10.2.30.140 with listen port 7890, then in the script.txt file, you should put in

==================
connect tcp://10.2.30.140:7890 &ltuser> &ltpassword>
shutdown
==================

The above sample script file can be used to shutdown EMS server gracefully using the following command,

tibemsadmin -script script.txt