The 400 HMRC customer service advisers are planning more action this week with industrial action set to last until June 2.
Ian Anfield, managing director of Hudson Contract, said: “Thankfully online verification of subcontractors under CIS has not been affected yet, but those wishing to newly register and those needing to speak to a human are reporting serious issues.
“The CIS verification process, and the queries that often come from it, are incredibly important for small firms and individuals because it is the process by which at-source CIS deduction rates are decided.
“Sometimes those with gross [zero deduction] will come back at 20%, and those with 20% deduction will come back at 30% when verified electronically. Only HMRC officers can sort these issues out.
“The upshot, if HMRC are not adequately manning the phones, is that some subbies will suffer higher than necessary CIS deductions, and given the tax year has just begun, they will have a long wait to get that money back next April – not great whilst small firms are fighting inflationary pressures, and during a cost of living crisis for sole-traders.”