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How can i fix the Index usage on one of our database server?

It says from our Nagios control panel that:

Service: DB Index Usage
Host: MySQL Cluster 
Address: ( our IP )
State: CRITICAL

Additional Info:

CRITICAL - index usage  90.01%
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Are you having performance problems, or are you just concerned about an arbitrary ratio set by the person who wrote a nagios check? – Aaron Brown Jun 26 '12 at 4:21
Yes i am just concerned about this alert! And this is the first time i encounter this. – Joey Jun 26 '12 at 4:58
Are you experiencing performance problems? Are there new queries in the slow log? – Aaron Brown Jun 26 '12 at 5:45
yes there is a lot of slow queries that need to optimize now.. – Joey Jun 26 '12 at 5:50
Then optimize the queries. This is a useless alert. – Aaron Brown Jun 27 '12 at 3:10

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