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I have found my self in a very confusing state.I am due to apply for my ilr on 5 years basis.I have recently contacted HMRC to get 5 years employment history and i found out that one of my previous employer has not filed my taxes in 2009.I was on a work permit with that employer and he gave me a certificate of sponsorship.The HMRC report states that i was employed by that company in 2009 but no taxes has been filed under my name.In Jan 2010 i moved to Tier 1and changed my employment and now i am employed with one of the biggest companies in UK.From 2010 to 2014 all of my taxes are filed as shown on p60.I have all my payslips and bank statements for last three years.
Can some one please advise if i should go for ilr based on the records i have but it wont match with HMRC for year 2009.The other option for me is to wait till december14 and complete 5 years on Tier 1 hence exclude the time i spent on work permit.Please advise.

1st it is not compulsory to submit last 5 years record to UKBA. you can give them last 3 or 4 years records as well.
and secondly if you have payslips and bank statement and P-60 for 2009 year you don't need to worry about. On employment income it is responsibility of the employer to deduct PAYE and NI of employee and deposit it to HMRC. If employer has deducted your tax and NI and didn't deposit to HMRC you can simply report to HMRC and send them your pay slips and P-60 as proof.
or 2nd option ask HMRC to send you a self assessment forms for 2009 and 2010 years fill those forms and attached copy of your all P-60 with those self Assessments and send it to HMRC.

Thanks a lot Malik for responding I guess I need to dig in and find whatever paperwork is avialable for 2009 I do have a p45. And letter from home office confining my cos and salary details. The strange part is that in homecoming records I was employed by that company until jab 14 but they filed minimum possible pay to avoid any taxes. Thanks again for looking into my query.

Hi Can i please have little more input from someone specially the senior members on this forum.

Were you present in the UK for more than 183 days in 2009? If not, then perhaps you were a non-resident for tax purposes during that year:

http://www.hmrc.gov.uk/international/residence.htm

I was in country for whole of 2009.I think its to do with my employer as you can roll back the payroll at the end of the financial year and file whatever you want with HMRC.in HMRC record i was employed by the company whole of 2009 but there is nothing in the tax and pay section.I guess i am in a bit of problem.Do you guys think i should get a professional advise?

Capricon - got ur ILR sorted ? Did the missing tax cause any issue for ILR?