Kate Forbes’s comments come after the UK and Scottish governments issued a joint statement agreeing there would be two “green freeports” in Scotland.
The ports will be special economic zones offering businesses tax breaks and free tariffs.
But the SNP Government’s partners, the Scottish Greens, have criticised the move for giving tax breaks and public money to multi-national companies in a row that was branded a “lovers’ tiff” by Scotland Office minister Iain Stewart.
Greens international development spokesman Ross Greer has described the plans as a “corporate giveaway” and a means of “greenwashing”.
Green freeports are excluded from the co-operation agreement struck between the Greens and the SNP.
The announcement has coincided with Boris Johnson’s visit to Rosyth in Fife on Monday morning – one of the sites viewed as a contender to become a freeport.
Mr Johnson denied the plans would simply displace investment and jobs, saying: “If you look at the attitude of the Scottish Government, it’s been fantastic. I think they’ve got the point and they can see the advantages of the freeports.
"I’m not allowed to give away the locations, but they can genuinely drive huge numbers of jobs and growth.”
The Scottish Government was initially against freeports, but Ms Forbes said four things had changed since the initial disagreement.
Speaking to BBC’s Good Morning Scotland, the finance secretary said: “Those are firstly that we will have equal say on the decision, so we are proceeding on the basis of a partnership of equals.
"Secondly, we will get full, fair funding. The funding for the green freeports has essentially doubled from what it was a few months ago.
"Thirdly, there are decarbonisation plans at the very heart of the green freeport approach.
"And lastly, and most importantly for us, fair work will be embedded at the heart of that. There will be a fair process.”
Mr Stewart said he agreed with the Prime Minister the ports would make a “transformational impact” across the UK.
He said the plans were expected to create additional economic activity of £25 billion.
He said: "This forms part of our long-term vision of the economy, particularly as we look to grow back after the restrictions of the pandemic.”
“The freeports in England have already been announced and the freeports in Scotland will be jointly decided by both governments.
"Some of the levers are devolved in Scotland and that’s why quite rightly we had a good negotiation with the Scottish Government.
"If this is a case of a lovers’ tiff on Valentine’s Day between the Greens and the SNP, then that’s not for me to intrude in.”
Mr Stewart said freeports would be subject to annual audits and high standard regulations to tackle any possibility of fraudulent activity.
All applicants for the freeports will have to lay out how they intend to implement fair working practice, including the real living wage, with the bidding starting from next month.
Ms Forbes said she hoped the greenports would be operational by the end of this year.