It has proposed setting up a new Scotland-wide statutory board to co-ordinate the activities of Scottish Enterprise and Highlands and Islands Enterprise (HIE).
The government said services already provided in the Highlands and Islands would be protected.
A new service has also been proposed for the south of Scotland.
The activities of Scottish Enterprise and HIE include the running of Scottish Development International, Skills Development Scotland and the Scottish Funding Council.
The Scottish government carried out a review of enterprise and skills support earlier this year.
It examined the roles, responsibilities and relationships of HIE and Scottish Enterprise.
HIE supports businesses and promotes economic growth in the Northern Isles, Western Isles, Highlands, Moray and Argyll.
It began as the Highlands and Islands Development Board 50 years ago. HIE was established in 1990.
The CairnGorm Mountain ski resort and its funicular railway is among the assets it manages.
A report on the first phase of the review of enterprise and skills services has been released.
The contents of the report are due to be debated at Holyrood on Wednesday.
Concerns about the future of HIE have already been raised by Highlands MSPs David Stewart and John Finnie.
Mr Stewart said he would oppose any move to merge HIE with Scottish Enterprise.
Earlier this month, in a response to a question from Mr Finnie, First Minister Nicola Sturgeon said the Scottish government would make sure HIE could continue to provide its services.
Following the release on the new report, Economy Secretary Keith Brown said: "We are proud of our enterprise and skills agencies, and in recent years their efforts have contributed to real improvements in our economic performance.
"But we know that further improvement is required - our ambition is for Scotland to rank among the top-performing OECD nations for productivity, equality, sustainability and wellbeing.
"Since the review was announced, the EU referendum result has made the economic context more challenging. It requires that we renew our focus and prioritise our efforts.
"This review has focused on how we can build on existing strengths and successes to further improve the enterprise and skills support system in Scotland.
"This will ensure a system in which all of our agencies work both hand in glove with each other and collaboratively with our business, academic and civic partners to optimise economic impact across the whole of Scotland."
Scottish Conservative economy spokesman Dean Lockhart said: "While I am pleased that the SNP have followed our lead once again in suggesting a South of Scotland enterprise agency, a lot more needs to be done.
"Our enterprise agencies are already doing a great job in encouraging business growth, but as Audit Scotland have said, it's the Scottish government that is holding them back.
"They need far more support in the work that they do, and a clear plan on exactly how the Scottish government want them to deliver its economic strategy."

Several of Cathro's recent signings are from various countries abroad, leading to some questioning their appreciation of the standards fans expect.
"This is tens of thousands of people's Real Madrid," said Cathro.
"Everybody understands clearly the size, the importance, how much love and passion there is for this club."
Hearts remain in fourth place in the Premiership but have gone four games without a victory.
Last week's Scottish Cup defeat by city rivals Hibernian, who are in the Championship, was followed by a top-flight defeat away to Partick Thistle.
More to follow.
The Scottish government has set out plans to reform Scotland's enterprise and skills agencies.
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Hearts head coach Ian Cathro insists his players have a full understanding of the size and magnitude of the club they represent.