He hit out an an "extraordinary" move by Foreign Secretary Jeremy Hunt to withdraw UK Government diplomatic support for the Scottish First Minister on trips abroad.
Mr Hunt has said this would apply when Ms Sturgeon is using trips to promote independence.
The Scottish Government has its own consul offices around the world, including the US, Brussels and Beijing which could facilitate trips without the Foreign Office, the spokesman said.
"Whatever happens it's not going to stop the Scottish Government and the First Minister representing Scotland internationally," the spokesman added.
He went on: "The First Minister will not be prevented from saying what she thinks in terms of Scotland's future - that's the essence of being a democratically elected leader.
"The First Minister will go on making the case for independence."
But he added: "It's entirely legitimate for the democratically elected First Minister to espouse the view that she was democratically elected on.
"If Jeremy Hunt's position is that Scotland shouldn't be afforded the same level of representation overseas as the rest of the UK, then he's making our case for us.
"He's in the most visible way possible making the arguments for independence."
But it would be "naive" to think Mr Hunt's stance was not connected to the Tory leadership race - and may "fizzle out" after this is over.
"The jury's out on that one," Ms Sturgeon's spokesman added.
A row broke out earlier this month following the revelation that support was withdrawn for a trip to Brussels earlier this month in response to concerns about her summer visit to the USA and Canada last year.
Mr Hunt said he would no longer sign off on help for trips that "give a platform for independence".
"I believe in the Union with every fibre of my being and British government policy is to protect, preserve, cherish and enhance that Union," the Foreign Secretary told the Daily Mail.
"So we are not going to offer support to Nicola Sturgeon if she goes abroad to drum up support for independence, and that is exactly why I am the Prime Minister that she least wants because she knows I won't allow our Union to be broken up."