Scotland's Culture Secretary Fiona Hyslop said she fully expected "long established arrangements for loans, exchanges and partnerships" to continue if there is a yes vote in September.
Her comments follow remarks by the director of the National Gallery in London, Nicholas Penny, in relation to two Titian paintings.
The works were jointly purchased for a total of £95 million by the National Gallery in London and the Scottish National Gallery, and are currently on display in Edinburgh.
The galleries bought Diana And Actaeon in 2009, using funding which included £12.5 million from the National Gallery in London, £4.6 million from the National Galleries in Scotland, and £12.5 million of Scottish Government grant money.
A second painting, Diana And Castillo was bought in 2012.
They were transferred to Edinburgh in August 2013 for 12 months. Following this both paintings will be shown together on a rotating basis in London and Edinburgh.
Mr Penny said that "in terms of pictures, (the referendum) calls into question the whole business of the division".
"We bought the two great Titians together so we share them. It would be very difficult to say that that was an entirely Scottish collection."
Ms Hyslop said: "The Titian paintings were purchased jointly by the National Gallery in London and the Scottish National Gallery and any suggestion that shared ownership would not continue in the event of independence is plain wrong.
"Scotland currently owns a share of all UK national collections with national museums and galleries in both London and Scotland holding items from different parts of the UK and collections assembled from across the world.
"There are a number of long established arrangements for loans, exchanges and partnerships, which I would fully expect to continue with the rest of the UK post March 2016."