Manoj,
Might help if we knew more about the environment.
Which version of the CA APM agent?
Which Application Servers and versions?
It might also help if you look into the agent's autoprobe and introscopeagent.log for the agent and see if you see any errors or non-typical behavior. In Autoprobe, you want to look to see if the agent is reinstrumenting often by searching for a single pbd file and seeing how many times the agent loaded it.
In the IntroscopeAgent log, look for errors in the communication to the collector.
In the application, look to see if there are a high number of error traces and what is causing the error traces.
We had two issues, one with version 10.0 and another with 10.5.2.
In 10.0, WebLogic running Oracle JVM 1.8, we hit two issues. One with the WebLogic Diagnostics Framework (byte instrumentation) and with the Oracle JVM 1.8 java script engine (nashorn).
In 10.5.2 we found that the SOA performance Management (SPM) was enabled by default within the base agent and that the SPM was not compatible with WebSphere 7.0.
For the JVM, how does the CPU and Memory (garbage collection) look like? If there isn't enough CPU or memory the agent will multiply the impact/effects and drive much more CPU than typical. If there isn't enough Memory, or too much memory, the Garbage Collection is going to be more often or has to compress more of the fragmented memory. Both of which would drive CPU.
How is the network looking on the JVM (agent) host side?
What is running within the JVM? Web Applications, Services (EJB), Services (SOAP)?
If you are using the typical PBL, that is "typically" all the general elements without any of the really deep stack tracers.
If you are running version 10.5.2+, try to comment out the SPM pbd out of the IntroscopeAgent.profile.
Hope this helps,
Billy