Board members have decided to keep Johnstone in Renfrewshire, with the two others chosen from Edinburgh, Dundee, Aberdeen and Inverness, following a consultation and further investigations over the next three months.
At a meeting in Aberdeen, they rejected by six votes to five the idea of moving towards just two centres, at Johnstone and Dundee.
It was the only change they made to a proposal entitled Strategic Intent, which includes the establishment of a single national training centre at Cambuslang, near Glasgow, and a national headquarters "located in the area bounded by Perth, Glasgow and Edinburgh".
The service was also criticised for a decision to axe the Scottish Fire Service College at Gullane, in East Lothian, and other properties.
It follows the merger of eight fire and rescue services into a single national service in April.
There is a commitment to avoid compulsory redundancies in the rationalisation process, which is projected to make savings of around £4.8 million a year.
Chairman of the Board Pat Watters said: "I recognise that the plans will affect a number of our staff and naturally everyone is concerned when there is change. It is important to stress these changes will take a number of years and we will be working closely with staff and representative bodies as we develop implementation plans."
Chief officer Alasdair Hay said "What we are aiming to achieve is that, as a national organisation, we ensure that we have the right facilities across Scotland to allow us to deliver our vital frontline services."
Board member Dr Michael Foxley, former LibDem leader of Highland Council, who fought to keep three centres, with at least one in Aberdeen or Inverness, said: "Local knowledge is often undervalued, but it is vital. We learnt lessons for the campaign to keep the coastguard stations."
The Fire Brigades Union's Scottish chairman Alan Paterson said he would have to consult his members on the detail once the union had a chance to examine it.
"Then both sides can get back into some meaningful discussions and negotiations with service managers. On any proposals, when it comes to the details, it's difficult to measure of what degree the risk is."
Labour's justice spokesman Graeme Pearson said: "Of course it's important that the merger of the fire boards leads to relevant efficiency savings but there also has to be consideration of the wider economic impact.
"I'm concerned that these decisions have been rushed through and there hasn't been any thought on what happens in the local communities where the call centres were."
He said he would also like reassurance that the closure of centres wouldn't lead to any dip in service. He added: "When people call 999 for the fire service they rightly expect that the help they require is dispatched as expediently as possible."
East Lothian Labour MSP Iain Gray said a proposal to shut the Fire Services College in Gullane was "unacceptable" and another blow to the local economy after the decision to close local courts.
He said: "The college occupies a prime site in one of the most attractive villages anywhere in Scotland, and now the Scottish Government are going to leave it as a vacant lot."
The Scottish Government said the strategy was a matter for the fire service board.