It sounds like you have FMG configured to track hitcount on policies in policy packages, which is known (prior to the most recent patches) to have some performance concerns (as noted in bug id 452464).
The fix in 5.4.4 & 5.6.1 (ETA, end of November) is to disable generating event logs on the FMG every time the hitcount changes.
1) disable hit-count from the System Settings > Advanced Settings
2) on the FortiManager CLI, filter out the objcfg logs (corresponding to the huge amount of event logs we're receiving) as follows:
config system locallog disk filter
set objcfg disable
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