Regarding the penalty for late filing

In FY 2008-2009 (AY 2009-2010), my gross profit was in 10% tax slab. But after computations my aggregate income was below Rs 1,50,000.

This month I'm going to file 2009 Return. I have found out that under section 271F, there is a penalty of Rs. 5000 for late filing. So is it applicable in this case? If yes, then should I voluntarily pay the penalty of Rs. 5000? or should I wait for any notice?

Thanks.
 

(Edited for clarifications)