When you see the problem manifesting, go to Troubleshooting Support tools page and generate a support .zip. Make sure to include Thread dumps in it (I think disabled by default).
Opening a case with Atlassian support they should be able to analyze the logs/dumps and point you in the direction what's causing the high CPU usage.
They will also probably ask you to run a thread dump on your server to pinpoint that a little better, but that's the second step.
If you cannot see anything out of the ordinary, such as maybe an import or re-index running, nothing suspicious in the logs, then contact the support - they have tools to do some quick analysis.
Basically the application logs and thread dumps are good to start with. Secondly you might want to check if your database server also has high cpu usage itself - which could narrow down the "nature" of the problem. For example we had a problem with one of the addons in the past causing CPU spikes and it turned out it had really terrible SQL command running almost constantly eating up the resources. This was apparent in the thread dumps that the plugin was consuming a lot of threads, and on the database that it was constantly calling humongous sql queries.
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