The administrator user is also used by certain applications to connect to the SAP J2EE Engine and perform certain tasks, for example, the Software Deployment Manager (SDM). These applications do not have direct access to the database, the database connection information, this user ID and its password are stored in a secure storage file in the file system.Therefore, if you change the administrator user’s password, then you have to update the entry in secure storage.

If you have to change the password for  SAP Java Administrator user ,follow following steps.

1. Activate emergency user.
2. Login with emergency user and  unlock /reset Administrator user password via User Administration
3. Deactivate emergency user.
4. Maintain the new Administrator password in secure store.

1. Activate emergency user.

To activate SAP* emergency user follow this tutorial.

2.Login to portal with emergency user and  unlock /reset Administrator user password via User Administration.

2.1  Access User Administration application by using following url :

http://<hostname>:5<xx>00/irj/portal  OR  http://<hostname>:5<xx>00/useradmin

2.2 Now go to Identity Management and look for user "Administrator". 

2.3 Now select that user and press "Unlock OR Generate New password" button.

3. Deactivate emergency user 

To deactivate SAP* emergency user follow this tutorial.

4.Maintain the new Administrator password in secure store.

4.1 Login to portal with Administration user and new password. If system prompts you to change initial password, change it and note down.

4.2 Now we will login to configtool to update the new password in secure store.

4.3 Launch Configtool - Go to to /usr/sap/<SID>/JC*/j2ee/configtool/ and execute configtool.sh (On UNIX like environment , please setup DISPLAY as per X11 /Reflection application).

4.4  Select secure store.

4.5  Select the admin/password/<SID> entry.

4.6  Enter the administrator user’s new password in the Value field and press Add.

4.7 Now press "File" -> "Apply" to save data.

In case  You are able to login with SAP Administrator  and want to change the password , follow following steps 

1. Login with Administrator user and change the password in identity management.(shown above)

2. Maintain new password in secure store.(shown above)

Reference

http://help.sap.com/saphelp_nw04/helpdata/en/99/281540bf1af72ee10000000a1550b0/content.htm