Les Montgomery, chief executive of the bottled water firm, said over the weekend that Scottish Business chiefs are "fed up" with Ms Sturgeon's quest for independence and want her to get on with the day job.
But the firm has now apologised in a statement, insisting the comments were not intended as an opinion on whether Scotland should be independent.
The company also confirmed to Insider website that it had been contacted by the Scottish Government in response to the original comments.
Economy Secretary Keith Brown insisted it was part of the “day job” to liaise with the firm in light of the concerns raised.
The original comments met with an angry backlash and threats of a boycott from Nationalists on social media with singer Eddi Reader among those indicating she would stop buying the firm's products.
Labour is now calling on the Scottish Government to set out its role in the affair.
"During the independence referendum we saw serious allegations of intimidation of business levelled at the SNP government. It was completely unacceptable then and would be unacceptable now," he said.
"The SNP government needs to clarify the nature of this contact and guarantee that businesses are not being silenced because of completely valid positions on government performance."
But Mr Brown played down the significance of the Government’s intervention today.
He tweeted: “Hearing concerns of HS (Highland Spring), I asked officials 2 c if they’d like 2 discuss them further..they do.
“Seems like the day job to me.”
The original comments from Mr Montgomery emerged on Sunday and saw him urge the Scottish Government to focus its effort on achieving the best possible Brexit outcome.
He said: "Businesses are fed up. The Scottish Government should be getting on with the job they are there to do. Focusing on employment, investment, those kinds of things."
"Independence isn't the job that the Scottish Government is supposed to be doing."
But in a statement issued yesterday sought to defuse the row.
"The comments being referred to came from a recent business news story which focuses on the importance of maintaining a 'business as usual' stance in light of recent political activity across the UK," a Highland Spring spokeswoman said.
"The statements made did not mention indyref2 and were not intended to offer an opinion on whether Scotland should or shouldn't remain a part of the UK; from either the perspective of Highland Spring or any individual member of staff.
"Instead, they were intended to outline a view that it is key for businesses in Scotland to have stability and clarity around ongoing important political issues, for the good of the Scottish economy and businesses. We're sorry if people have taken this the wrong way."
A spokeswoman for the firm confirmed to the Insider that the Scottish Government had contacted the firm in response to the original comments, but declined to say whether this was from a minister or a civil servant.
She said: “Highland Spring are always happy to have regular conversations with the Scottish Government, we enjoy an open dialogue [with them].”