In the first major split between the SNP and the Scottish Green Party since they signed their powersharing deal last year, the Greens have criticised plans to create the special economic zones which offer firms tax breaks and lower tariffs.
Last year the Scottish Government said Westminster risked undermining devolution if they set up freeports in Scotland and Wales without the backing of devolved governments.
Ministers in Edinburgh later said they would pursue an alternative model called “green ports”, but under the new deal they will be known as “green freeports”.
The Scottish Government said the term “green freeport” reflected its distinctive net-zero aspirations.
But Mr Greer said: “A little greenwashing won’t change the grim reality of these ‘freeports’.
“They are yet another way of handing tax breaks and public money to rich corporations, despite no evidence that it will create real economic prosperity.”
The deal between Holyrood and Westminster comes as Prime Minister Boris Johnson is expected to visit Scotland on Monday.
Mr Greer added: “Instead of working with the Tories, we’d urge SNP colleagues to collaborate with those of us who want to build an economy which serves, rather than exploits, people and planet.
“They certainly know where to find us and our door is always open.”
The UK Government has committed funding of £52 million to the project and bidders will have to pledge to reach net zero by 2045.
Ministers from both governments will have a say in the assessment and selection process for the bids.
The Scottish Government and the Treasury will use their tax powers, including rates relief, to support the freeports.
Under the UK Government's model, freeports are centred around at least one air, rail or sea port, but can extend up to 45km beyond.
Mr Johnson said: "Freeports will help to accelerate our plan to level up communities across the whole of the United Kingdom.
"They have the power to be truly transformational by creating jobs and investment opportunities to enable people to reach their potential, and I am delighted that people across Scotland will reap the benefits that will come from having two new green freeports."
Levelling Up Secretary Michael Gove said: "This is a truly exciting moment for Scotland, and I am delighted we will be working together with the Scottish Government to set up two new green freeports.”
Scotland's Finance Secretary, Kate Forbes, said: "I am pleased we have been able to reach an agreement on a joint approach that recognises the distinct needs of Scotland and enshrines the Scottish Government's commitment to achieving net zero and embedding fair work practices through public investment."
The Scottish Government said the term "green freeport" reflected its distinctive net-zero aspirations.
Ian Murray, Labour's shadow Scottish secretary, said regions in England had a head start "because the two governments disagreed over the name".