Go to GUI of the Wireless Controller -> Controller Tab -> General -> AP Fallback -> Change it from Enabled to Disabled -> Click on Apply and then Save configuration.
Then go to the Wireless Tab on the GUI of the wireless controller -> Click on the AP name which is disassociating from the controller frequently -> Click on the High Availability Tab -> Set the Primary Controller name as the System Name of the controller to which this AP is supposed to Join, put the Management Interface IP address of this controller and then click on Apply and Save Configuration.
Go to the Wireless Tab on the GUI of the controller -> Under Access points -> Click on Global Configuration -> High Availability -> enable flex connect mode AP Fast Heartbeat -> Set the fast Heartbeat Timeout to 5 or 10 seconds.
Click on Apply and Save configuration.
This resolved the issue and the AP's are no longer losing association with the Wireless Controller.