During today's Budget George Osborne confirmed that there will also be a new 2% rate for those high value leases with a net present value above £5 million.
The reforms are estimated to raise £500 million a year.
Around 9% of businesses will pay more, but over 90% will see their tax bills cut or stay the same, according to Osborne.
He said:
"At the moment, a small firm can pay just £1 more for a property and face a tax bill three times as large. That makes no sense.
"So, if you buy a pub in the Midlands worth, say, £270,000, you would today pay over £8,000 in stamp duty. From tomorrow you will pay just £3,000."
Mark Tighe, managing director, capital allowances tax specialists, Catax Solutions, said:
"The reduced stamp duty payable on commercial property announced by the Chancellor will doubtless drive demand in this key asset class in the months and years ahead.
"But the resultant increase in transactions, among both businesses and private individuals buying commercial property, will potentially cost billions as a largely unused tax relief is lost forever.
"Capital allowances are a highly valuable tax relief available to owners of commercial property but under current legislation they are irrecoverable if they are not identified and realised at the point of sale.
"Currently, very few commercial property owners, along with their accountants and lawyers, are aware of unused capital allowances tax reliefs.
"Therefore as transaction levels increase in volume and momentum, commercial property owners are set to lose significant tax rebates to the tune of thousands, tens of thousands or even hundreds of thousands of pounds."
