My employers has been sent an attachment of earnings order claiming unpaid council tax in 2001?

I cannot prove I have paid or not as no receipts kept, can they still chase this as a debt owed
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Yes; the statute of limitations doesn't apply to Crown debts. However, you can use your Data Protection Act rights to get the council to send you all the data they have regarding your account, if you believe that you are not liable for the debt.

You should have received a summons as the order would have been made by a judge. Why didn't you attend the hearing and state your case there?
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You must have been contacted about this many times before , probably chose to ignore the letters .. If you cannot prove payment . either by receipts, bank cheques or card statements ,, then you are due to pay . Generally the council records are pretty good and accurate, the probability is you didnt pay it .. So just pay up .. and make sure you keep all receipts and records . I do for 10 years ,
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The previous answers are both correct - just as an add on - your employer has absolutely no choice in the matter but to deduct money from your wages or face prosecution themselves.