Coastguard stations in Shetland and Stornoway have escaped closure as part of an overhaul of the service.
But the UK government has announced that it plans to go ahead with the closure of the Forth and Clyde bases.
The original proposals would have retained one 24-hour station in Aberdeen and a second base in either Shetland or Stornoway - which would only be open during daylight hours.
All three stations will now remain open round-the-clock.
The Forth and Clyde bases are now set to close at some point between 2012 and 2015.
The UK government said 31 jobs would be lost at the Clyde coastguard station.
Labour and the SNP have criticised the shutting of the two stations, while a separate campaign to prevent the withdrawal of coastguard tugs will continue.
Transport Secretary Philip Hammond told the House of Commons that the new proposals would both modernise the Maritime and Coastguard Agency (MCA) and achieve efficiencies.
He said 1,800 responses were received during public consultation on the original proposals to cut half of the 18 coastguard stations across the UK.
The new plans will also be put out to consultation, with 6 October set as the deadline for views.
Unions, campaigners, and a cross party committee of MPs said the original plans could put lives at risk.
Scottish Rural Affairs Minister Richard Lochhead said the original plan had been "reckless".
And a House of Commons transport committee report said safety would be jeopardised if the proposals went ahead.
In parliament, Labour MP Iain McKenzie said the west coast of Scotland had experienced an increase in shipping.
He asked Mr Hammond if he thought closing Clyde would compromise safety.
The transport secretary denied that it would.
But Scottish Labour said closing the coastguard centres on the Clyde and Forth would have a devastating impact on the local communities and put maritime safety at risk.
Shadow Scotland Office Minister Tom Greatrex MP said: "It's clear to me that the Tory-led government's decision to close nearly half of the UK's coastguard stations has nothing to do with improving safety along Britain's coastline but is a consequence of cutting the transport budget too far and too fast.
"Ministers must now carry out a full risk assessment of these closures before the further period of consultation takes place so that it can be properly considered before these closures go ahead.
"Safety in Scottish waters has to be the priority."
Western Isles SNP MP Angus McNeil added: "The decision to continue with closure of the Forth and Clyde stations is a real blow for the communities concerned."
The Scottish Conservatives and Liberal Democrats have welcomed the changes to the plans.
Orkney and Shetland Liberal Democrat MP Alistair Carmichael said: "Everyone in government from the prime minister downwards made explicit from the very start of the consultation process that ministers would listen to the concerns that people had over the MCA's original proposals.
"The announcement today shows that this was no empty promise."
Mr Carmichael added: "People in Shetland had a very clear view that nothing less than 24-hour stations in Lerwick and Stornoway would be acceptable.
"I took that message to the heart of government. Ministers have listened, responded and delivered. I am delighted."