The former Labour prime minister gave a speech in London on Brexit and the General Election and said Boris Johnson's deal - where Northern Ireland remains more closely aligned to the European Union than the rest of the EU - added "an additional dimension" to the nationalists' argument.
Speaking to a Reuters Newsmakers event on Monday morning, Mr Blair said: "I don't think campaigning for an independent Scotland is extreme. I just don't agree with it.
"I think the United Kingdom is stronger if we're all together, I think Scotland is better off inside the UK.
"But, you know, Brexit has put it back on the table again. This part of the other problem, I'm afraid, is that you've got a situation with Northern Ireland which is very tricky if the Johnson deal goes forward.
"You've got a situation where obviously the Scottish nationalists now have an additional dimension to their argument.
"I still don't agree with it, but, you know, they're going to be saying: 'You've allowed Northern Ireland to stay inside the single market, why aren't we allowed to, we also voted heavily against Brexit?'"