MSPs have voted to demand the Scottish government allow Highlands and Islands Enterprise to retain its own board.
The government wants a new management body to oversee all of Scotland's enterprise and skills agencies.
Opposition members say this would be a "death knell for HIE as we know it", and backed a motion asking the government to "reverse" its decision.
Economy secretary Keith Brown said HIE would "continue to be locally based, managed and directed" under his plans.
HIE supports economic growth in the Northern Isles, Western Isles, Highlands, Moray and Argyll.
The move is part of the ongoing enterprise and skills review, and would see a new Scotland-wide statutory board co-ordinating the activities of Scottish Enterprise, Highlands and Islands Enterprise, Skills Development Scotland and the Scottish Funding Council.
Lib Dem MSP Liam McArthur said ministers had been "arrogant and tone-deaf" over the plans, which he called an "ill-judged and dangerous" bid to "centralise the life out of" the region.
SNP MP Ian Blackford has argued that the local body should be allowed to retain its decision-making powers. He said that while he "fully endorsed" the establishment of a central board, HIE should have its own "management or advisory board" to "reflect the priorities" of the Highlands and islands area.
Prof Lorne Crerar, the chairman of HIE, has said the body would not be "in any way diminished" by the changes.
Scottish Conservative MSP Donald Cameron, who has previously described the board changes as "the death knell for HIE as we know it", put a motion forward during Tory debating time at Holyrood.
It asked MSPs to agree "that the parliament opposes the Scottish government's plans to abolish the board of Highlands and Islands Enterprise", while noting the "vital work" the group does and calling on the government to "reverse this decision and ensure that the HIE board continues to take all strategic, operational and budgetary decisions".
Mr Cameron's Conservative colleague Edward Mountain summed up his party's argument, saying: "HIE is not broken. It works. Stop trying to break it."
Labour's Rhoda Grant, backing the Tory motion, described the government plans as a "power grab", saying their "only aim is centralisation". This was echoed by Mr McArthur, who said the SNP had "an unhealthy appetite for controlling every aspect of what goes on in this country".
'Exaggeration and hyperbole'
SNP members also raised questions, with Gail Ross asking if he would consider "some sort of mechanism that ensures local decision-making in the Highlands and islands".
However, another SNP member, Kate Forbes, said "the air is so thick with exaggeration, hyperbole and superlatives it's impossible to see the truth", adding that she was "quite disappointed opposition parties have spread such fear in communities with their irresponsible rhetoric".
Mr Brown said he was committed to making sure that the body would remain locally run.
He said: "I am happy to make an explicit promise to parliament and to businesses and employees across the Highlands and Islands that HIE will continue to be locally based, managed and directed, providing dedicated support to the Highlands and Islands economy.
"The review focussed on how we can best ensure that all our agencies are working together. Respondents said there was a complex and cluttered landscape which was often confusing for local people and businesses and that we needed clearer alignment of our services to deliver our national ambitions.
"That's why we will align these key agencies under a strategic Scotland-wide board - and also protect local decision-making, local management and local delivery."
An amendment from Mr Brown was rejected by MSPs, by 64 votes to 63.
An amendment by Labour's Ms Grant supporting the plans was passed, before the amended motion was also passed, both by the same margin.
Presiding Officer Ken Macintosh told members that the vote was not binding, but said it was down to the government to decide how to respond to the will of parliament.