I filed a paper partnership tax return on 5 November, and one for another partnership on 15 December, whilst using HMRC’s online filing system to file the self-assessment tax returns for the partners. The two partners of one partnership paid their tax bills in full prior to 31 January 2011. The other partnership, which ceased trading last March, received a tax rebate due to a trading loss.
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I would not be too hopeful
The basic facts are against you. If a partnership tax return is filed late, each partner is charged a penalty of £100, regardless of whether there is any tax liability or if any tax liability has been paid by the partners. Paper returns are due by 31st October, online returns by 31st January. By now, you are in a Catch 22 situation - if the penalties are not paid, either by you or the individual partners, HMRC will continue to chase the partners, but if you do pay, HMRC will probably ignore your appeal.
If you really feel that you have valid extenuating circumstances, I would:
appeal immediately with one letter for each partnership, but giving the UTRs for the individual partnerstell the partners in writing that you will pay their penalties (and interest) if push comes to shove, but to stand firm against the pressure from HMRC for them to pay.