The survey of 1,000 businesses by the British Chambers of Commerce (BCC) found that Britain's SMEs believe they are not given as much support from the Revenue as medium to large businesses, and that the rules are not applied evenly.
Almost half (49%) of businesses do not believe HMRC provides the requisite support they need to be compliant, while two thirds (67%) think the Revenue does not apply tax rules fairly across all business.
"There is also widespread disappointment over the escalating burden of up-front taxes and costs of doing business in the UK, particularly at this time of heightened uncertainty. This has proved to be the tipping point for many smaller firms who typically operate on a tight cashflow", said Suren Thiru, head of economics at the BCC.
"HMRC must step up efforts to provide better support to smaller businesses to get their tax right, rather than simply pursuing and enforcing penalties. This should include matching investment in frontline HMRC help towards SMEs, with their work on non-compliance and tax evasion", he added.
HMRC has been criticised recently for "having inadequately considered the needs and concerns of smaller businesses" during its rollout of Making Tax Digital for VAT.