Ministers did not make the decision to sack the bosses of CalMac and Ferguson Marine, Humza Yousaf has said.
The First Minister also said he wants all agencies involved to have a “laser-like focus” on delivering for island communities.
He said he has confidence in the chief executive of Caledonian Maritime Assets Ltd (CMAL) – the Government’s company which owns the ferries and port infrastructure.
It emerged on Wednesday that CalMac chief executive Robbie Drummond had been removed by the state-owned ferry operator’s board.
As an interim replacement was announced, the UK’s largest ferry operator said there are likely to be ongoing challenges on the west coast network until new vessels join its fleet.
Mr Drummond’s departure came a week after the chief executive of shipyard Ferguson Marine, David Tydeman, was sacked by the state-owned company’s board. Ferguson Marine is building two over-budget and delayed ferries for CalMac.
Mr Yousaf addressed the matter on Thursday as he visited Dingwall Mart in the Highlands with the SNP’s candidate for the Caithness, Sutherland and Easter Ross seat, Lucy Beattie.
He was also joined by SNP ministers Emma Roddick and Maree Todd, as well as backbencher and former leadership rival Kate Forbes.
Asked if Wellbeing Economy Secretary Mairi McAllan or other ministers had ordered the sackings, Mr Yousaf told the PA news agency: “No, these are independent decisions by the board.
“Let’s be clear – both Mairi and I have been very clear with boards, be it the board of Fergusons, be it our colleagues at CMAL or CalMac, that we expect delivery.
“We expect there to be a laser-like focus on delivery for our island communities.”
Mr Yousaf said he has confidence in CMAL boss Kevin Hobbs.
He added: “Any decisions around the management are for the board of these organisations to make.
“Our direction – from myself, from Mairi McAllan and the Transport Cabinet Secretary Fiona Hyslop – is very clear.
“Focused on delivery, and that’s really crucial not just for the Government and for the organisations involved, but importantly for the island communities we seek to serve.”
Ministers want to return Ferguson Marine to the private sector “when we possible can”, he said, meaning there would inevitably be some “restructuring” of the various ferry organisations the Government owns.
Following Mr Drummond’s departure, opposition parties said SNP ministers are presiding over “chaos” on the ferry network, and demanded further answers from ministers.
In recent years the ageing nature of CalMac’s ferry fleet has led to delays and disruption on its routes around the west coast of Scotland.
These problems have been compounded by ongoing delays to the two ferries being built at Ferguson Marine in Port Glasgow.
The vessels, which will ultimately serve routes in the west of Scotland with CalMac, are currently running some six years late and will cost around three times the original price of £97 million.