The Labour leader said at the weekend that he would be "absolutely fine" with a vote being held.
And he said it was "not the job of Labour to stop people holding referenda".
But speaking to the BBC's Today programme on Monday morning, he insisted that a referendum should not be held.
He was speaking as Scotland's first minister, Nicola Sturgeon, prepared to make what has been described as an "important" statement on Brexit.
There has been speculation that Ms Sturgeon will use her speech to outline plans for a second independence referendum - although she would need the consent of both the Scottish and UK parliaments in order to make it legally binding.
Holyrood currently has a narrow pro-independence majority, but Prime Minister Theresa May has so far avoided saying whether or not Westminster would give its permission for a vote to be held.
Mr Corbyn told the Today programme that it would be "wrong" for the UK Parliament to block another vote going ahead if the Scottish Parliament was in favour of it.
He added: "But let's be absolutely clear, I do not think there should be another referendum, I think that independence would be economically catastrophic for many people in Scotland.
"It would lead to a sort of turbo-charged austerity with the levels of income the government has in Scotland and because of the very low oil prices and the high dependency on oil tax income."
Mr Corbyn had been in Glasgow on Saturday to speak at Labour's economy conference when he told the Press Association that he would be "fine" with a second referendum.
His weekend remarks were immediately condemned by senior Scottish Labour figures, with the party's only MP in Scotland, Ian Murray, accusing Mr Corbyn of "destroying the party".
Scottish Labour's economy spokeswoman, Jackie Baillie, said Mr Corbyn's comments had been "misguided and irresponsible".
She added: "They are an insult to the dedicated work of Scottish Labour MSPs, councillors, and thousands of activists who have campaigned against a divisive second referendum."
Ms Sturgeon tweeted that it was "always a pleasure to have Jeremy Corbyn campaigning in Scotland" - accompanied by a laughing emoji.
Jeremy Corbyn has sought to clarify his position on a second Scottish independence referendum.