An independent accountant is hired as an 'agent' of a business, meaning that they carry out work on that company’s behalf. HMRC takes the view that, although the accountant has made the error, it is the company itself that is liable for any fines or penalties arising from these unfortunate circumstances. Final responsibility and liability for the accuracy and timeliness of tax returns and other document filing rests with your company. If your accountant has been blatantly unprofessional or has little practical experience of dealing with limited company accounts, you may choose to look for a replacement. You could also make a complaint against them via their professional accountancy body.