Yesterday, he ruled out a short-term solution for controversial plans that are expected to see a number of the offices shut across the country.
Both police and fire services announced earlier this year that several control rooms will be axed in the single-force shake-up.
Sir Stephen, speaking during a trip to Aberdeen to open a refurbished police office, said the possibility of shared facilities in the future was an idea he and Scotland's chief fire officer Alasdair Hay agreed "made sense".
He said: "We both agree that the long-term future - the next five or 10 years - could well see combined control rooms across Scotland. It would make sense.
"But we are just not there yet. We have to rationalise our estates first and make them as effective as possible individually.
"Then we can look when it comes to building the new buildings, making them big enough to look at combining fire, police and possibly ambulance and other agencies."
Sir Stephen's comments come days after trade union Unison announced that Scottish police staff are to be balloted for industrial action following last April's move to a single force.
The union claims trust between Police Scotland and trade unions has broken down.
One of the main points of contention has been the Scottish Police Authority's proposals to axe half of the country's contact, command and control centres, which handle 999 calls.
A total of five police control rooms - Glasgow, Stirling, Glenrothes, Dumfries and Galloway, and Aberdeen - have been earmarked for closure.
He said: "The reassurance I can give is that we haven't done this without a great deal of thought.
"We are very confident from the analysis that we have done that it will provide a very good command, control and dispatch system for policing across all of Scotland."