John Swinney cautioned Nicola Sturgeon against calling for a second independence referendum on the day of the Brexit result.
Speaking to the BBC, the now First Minister said he was anxious that voters would not want to come out for a third plebiscite in as many years.
At the time he was Ms Sturgeon’s deputy.
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While the UK voted 52% to 48% to leave the UK, Scotland voted 62% to 38% to remain.
Mr Sturgeon wrote a speech in which she said a second independence referendum was now “on the table.”
Mr Swinney told the documentary: “And I can remember saying to Nicola as she was formulating the message she was going to convey in the aftermath of the Brexit referendum – was she sure that she wanted to say so firmly that she was opening up dialogue about a further referendum.”
He continued: “I have to say I was nervous, because I was still concerned by how we were able to motivate people in Scotland when we had just had one (a referendum) in 2014.”
Mr Swinney’s comments came in an interview for Salmond and Sturgeon: A Troubled Union, a new documentary looking at the rise of the SNP and the fallout between its two most successful leaders.
(Image: PA)
The show features a host of interviews with senior figures, including the last four first ministers and many of their aides.
Other revelations include Alex Salmond telling Nicola Sturgeon in 2014 that her husband, Peter Murrell, should step down as the SNP’s chief executive.
He told the show: “After I stood down as leader, I thought it was my job to tell Nicola first and then Peter I thought the combination between her being the first minister and Peter being the chief executive was going to cause great difficulty, not necessarily when things were going well, but as soon as things went badly.
“It was going to be a relationship which the press would exploit.”
Ms Sturgeon said she “took a different view.”
“Peter had done the job as Chief Executive a lot longer than, you know, way before I became first minister.
“I think if the gender roles had been reversed, and the idea a woman had to step down from their job because of their spouse's role, that would have looked odd.”
Mr Murrell was forced to quit last year in a row over party membership numbers. Earlier this yea he was charged with embezzling party funds.
The show also reveals that a number of senior figures in the party blamed Salmond’s remarks about Nato action in Kosovo in 1999 for their poor result in the first Holyrood election.
Mr Salmond said the military action was "an act of dubious legality, but, above all, one of unpardonable folly".
“The language was language I thought was just not appropriate, not correct. I just thought, Oh, this is the last thing we need at this stage. And the reaction was just terrible,” John Swinney told the programme makers.
“The few days after that were really, really tough,” Ms Sturgeon said. “I certainly felt that any outside chance I had had of winning Govan probably evaporated.”
In the end, she lost to Labour’s Gordon Jackson, but was returned to Holyrood on the list.
“Looking back, I think I was right,” Mr Salmond said, “But at the time, it wasn't the most convenient thing to say, as you started the Scottish election campaign.”
Mr Salmond also criticised the team around Nicola Sturgeon during her time as First Minister, saying he didn’t “rate them highly”.
Mr Sturgeon said her relationship Mr Salmond changed suddenly in the wake of the 2017 general election when he lost his Gordon seat to the Tories.
“He didn’t take my call for two weeks afterwards,” she said. “Suddenly I felt he was very deliberately rejecting me and punishing me for whatever he thought I had got wrong.”
The first episode of A Troubled Union will be broadcast on BBC Scotland at 10pm on Tuesday.
The second episode will be broadcast at the same time on Wednesday and feature the criminal case against Mr Salmond, where he was cleared of sexual assault.
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