The Government Gateway tax computation and filing tool includes a section/disclosure on Off-Payroll Working (OPW) (please see attached). TaxFiler does not have any way of tracking this, meaning CT600's can look incorrect when compared to Ltd company accounts.
A Ltd company contractor who contracts via an intermediary agency to a public sector body needs to disclose what company income/drawings/salary has already been taxed via PAYE, and is therefore not subject to Corporation Tax.
The only way to submit this situation currently in Taxfiler and get the correct calculation is either to omit it alltogether, so the revenue and costs don't match the accounts. Or include it in revenue and staff costs without informing HMRC that some of revenue and staff costs have already been taxed via PAYE within IR35. Either method is not displaying a 'true and fair' view, unless there is something disclosing the Inside IR35 amounts to HMRC.