The polling expert pointed to the voter share enjoyed by both sides of the constitutional argument and claimed it now “dominated” how people voted.
Speaking at a UK in a Changing Europe 'Spotlight on British politics’ event on Monday, the University of Strathclyde professor explained independence was also a bigger factor than Brexit.
He said: “What is absolutely intriguing, which has meant that neither side has really been able to claim a clear victory in this election if you add up all the votes cast for the parties in the constituency election, 50.4 per cent were cast for parties that were in favour of staying in the union and on the list vote, then 50.1 per cent of the vote was cast for parties that are in favour of independence.
"In other words, which party people voted for and their view on independence are virtually synonymous with each other.
“It frankly confirms that we are in a situation where half of Scotland roughly speaking wants to be independent and half wishes to stay inside the UK.
“So the country's divided down the middle and it's also deeply polarised on this subject and it does therefore present politicians, whatever their constitutional preference, with quite a considerable challenge as to how in the end you are going to resolve what ultimately is one of the most difficult issues to resolve in politics, which is an issue of legitimacy.”
A survey undertaken by Savanta ComRes for The Scotsman and published on Sunday had shown one in five (19 per cent) of voters in the Holyrood election said they had voted tactically.
Seventy per cent of those surveyed said they had voted for the party they wanted to see win and a further 9 per cent stated they voted for another reason.
Sir John explained support for independence and the SNP were now “virtually synonymous” with each other, and agreed tactical voting had been crucial in preventing a majority.
He said: “That was reflected in particular on the unionist side in a very clear evidence which has now be confirmed by polling data published yesterday of those on the Union side of the argument being willing to vote for whichever party was best able to stop the SNP from picking up a number of marginal opposition held seats.
"[It is] a development that was crucial in ensuring that the SNP did not get the 65 seats that they wanted and therefore an overall majority.”
Sir John also questioned the approach of the UK Labour party, accusing them of failing to act on the government’s mistakes.
He said: “It’s just got to stop being so timid. It’s not just keep schtum on Brexit, it has seemingly had virtually nothing to say about anything.
“It’s not coming up with virtually anything in the way of alternative proposals.
“At the end of the day the art of effective opposition is not just simply pointing out the weaknesses in what the government is doing, but it is then to link that with a message of how you would do things better.
“To that extent at least therefore it has been inviting people to vote for a vacuum, and inevitably that’s not very attractive.”