In March, Mr McColl said he would not have signed the deal had he known Caledonian Maritime Assets Limited (CMAL) had reservations.
He claimed the Port Glasgow yard had not settled on a price with CalMac ferries owner CMAL when the contract was announced and has since called on Ms Sturgeon to lift non-disclosure agreements, which he claimed were preventing former managers from speaking out.
Addressing these comments, Ms Sturgeon told Good Morning Scotland on Monday: “I think this is disingenuous in the extreme because the issue we are talking about here was Jim McColl’s company’s refusal or failure not to provide what the initially said they would provide, which is a full refund guarantee.
"Now if Jim McColl is saying he wasn’t aware of that at the time and wasn’t aware of the concerns that were expressed, then I just find that a bit strange.”
Ms Sturgeon said it was “manifestly not the case” there was no documentation around the decision making of the contract.
During First Minister’s Questions last week, Ms Sturgeon said only one piece of documentation was missing, but the decision was clear from the surrounding documentation after Scottish Tories leader Douglas Ross said the ferries row looked like an "almighty cover-up".
The First Minister also said the shipyard at Ferguson would have “almost certainly closed and the 400 people employed there, earning a wage, supporting their families, would not be in that employment”.
Asked why two ferries were ordered by the Scottish Government despite CMAL advising the contract was a risk, Ms Sturgeon said there were “basic mitigations”. These included the amount of money withheld till the end of the contract by CMAL increasing and mitigations around asking suppliers to supply refund guarantees, the First Minister said.
Ms Sturgeon said “at every point” the Government has acted in a way to protect jobs and commercial shipbuilding at the Clyde.
She said issues with the delays to the ferries and their cost overruns were “deeply regrettable”.
Her comments came as former Scottish Tories leader Ruth Davidson said Ms Sturgeon was treating Scots as “fools” over the ferries scandal.
Ms Davidson said: “The SNP are more arrogant and complacent than ever before.
“The ferries scandal shows that Nicola Sturgeon thinks she can get away with treating the Scottish public as fools.”