Non-VAT registered firms face scrutiny.
Mitchell Charlesworth VAT manager Colin Corder urged firms across North Wales to take immediate advice if they are unclear on their VAT position.
He said all firms with a taxable turnover over pounds 73,000 must register.
"HMRC is set to investigate 40,000 non-VAT registered businesses," he said.
"Firms that have not registered but are found liable for VAT could face penalties of up to 100% of the tax owed on top of the existing sum owed and possible criminal prosecution."
Mr Corder said firms are particularly at risk if they are not taking regular accountancy advice.
"I often see businesses that do not know how and when to check if they have exceeded the VAT threshold," he said.
"As a result many businesses exceed the VAT threshold but are unaware they have.
"So the key message is to check and double check your VAT position with your accountant throughout the year."