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Hi,
I came to UK in Feb 2008 in Work permit visa (Intra Company) and completing 5 years in UK at Feb 2013. But in between there was a gap of around 386 days in 5 years.
Below are the details of absence (all are work related)

Feb 2008 to Feb 2009 - No
Feb 2009 to Feb 2010 - 134 days
Feb 2010 to Feb 2011 - 46 days
Feb 2011 to Feb 2012 - 206 days
Feb 2012 - current - No

Can I apply for ILR in this scenario according to new rule or needs to wait till May 2013 so that 206 days split between 2 years.Company will not give letter for these absense, please suggest if any alternate option

You definitely need an extension.

Already applied for extension, but is there is option for ILR without absense letter?

Not for tier 2 unfortunately....but I am sure if you get a generic letter from your hr explaining the new guidance and that it is mandatory to provide such a letter I am sure they will consider. Also, speak to your line manager and then let him request the same for you. Try and get a detailed letter is possible.