Revenue Scotland will be set up this year and be fully operational by 2015 to administer the Scottish versions of stamp duty and landfill tax devolved through the Scotland Act.
Finance Secretary John Swinney claimed the new body would be at least 25% cheaper than Her Majesty's Revenue and Customs (HMRC).
Labour said Mr Swinney had failed to explain why Scotland needed a "tartan taxman", and the Conservatives said it was a "big wheeze to create another quango".
However, Mr Swinney insisted Revenue Scotland would serve the needs of the people at a lower cost than the UK set-up and deliver "a better system more in line with Scotland's needs".
He told MSPs yesterday the cost for HMRC to administer the existing charges for the new land and buildings transaction tax and landfill tax on behalf of the Scottish Government up to the end of March 2020 would be around £22.2 million but the cost of the new system would be just over £16.7m.
He said: "It is a sign of the costliness of HMRC that we will both establish Revenue Scotland and implement and collect both of the replacement taxes for less than HMRC would charge us to deliver what they term a like-for-like system with the UK. I estimate that over the period to 2020, start-up and operational costs in pursuing this approach will be at least 25% lower than if I ask HMRC to deliver the status quo."
The new body is also being set up because HMRC could veto requests to collect the new landfill and property taxes if they differed too greatly from the UK system. Mr Swinney said that could mean the freedom of Parliament to take forward the tax responsibilities in full could be inhibited, a situation that "cannot be right".
The new body will work with Registers of Scotland and the Scottish Environmental Protection Agency to collect the new charges. Both organisations already have a role in this.
Although Scotland will also have new powers over income tax in 2016, this will still be collected by HMRC.
Labour spokesman Ken Macintosh said Mr Swinney's statement provided "very little on what most people want to know – whether the new taxes are going to be higher or lower than before".
He said: "The Scottish Government has said it wishes to cut corporation tax, over which it has no control, and yet it doesn't tell us what it intends to do over the taxes for which it has full responsibility."
Mr Swinney said there were nearly three years to go before the taxes were devolved to Scotland so "it would not make sense, nor would it be the practice of any other government, to consult now on tax rates that will apply so far in the future".
Tory spokesman Gavin Brown said: "The economy is in a mess, public services are being squeezed and the big wheeze from the Scottish Government is Revenue Scotland, a new quango to collect two taxes."
CBI Scotland director Iain McMillan said there was no reason why the tax should not be collected by Revenue Scotland if it resulted in lower costs, while Colin Borland, of the Federation of Small Businesses, said it must not create additional paperwork for businesses.