The Dark Blues are still three weeks away from their World Cup opener with Japan but Cotter is already taking the heat over his controversial squad selection.
In-form back-row duo Blair Cowan and John Barclay were both cut from the 31-man travelling party that heads to England in 12 days’ time after former All Blacks youngster John Hardie was drafted in just five weeks after touching down on Scottish soil for the first time.
The inclusion of yet another foreign recruit sparked fury among the likes of former Scotland prop Peter Wright, who dubbed the decision to snub native Scots such as Barclay a “disgrace”.
As well as specialist number seven Hardie – who qualifies through his Fife-born grandparents – there was also a surprise call up for Glasgow lock Tim Swinson, even though he missed almost all of the national team’s two-month training camp after ankle surgery.
But Scott has leapt to the defence of his coach after insisting the former Clermont Auvergne boss was the best placed person to make the tough calls.
He said: “Vern is a guy who is a great coach, he’s been in rugby for many years and he works with us every day.
“He goes through training with a fine tooth comb. He’s got a plan for us going to the World Cup. There is going to be disappointed guys and it’s a shame to see a lot of guys leave camp.
“But we are right behind the way Vern wants us to play. We are right behind his vision for us and if he thinks this 31 players is the right balance then I am completely behind him in that sense.
“Nobody pays any attention to (Cotter’s critics) – we’re just honoured to be in the position we’re in now. We’ve now got to go and make the country proud.”
Asked if those sniping from the sidelines should refrain from passing judgement until after the World Cup, Scott said: “Yeah. The main thing is that picking a squad is really subjective.
“When I watch other teams play I sometimes think, ‘Why aren’t they picking him or him?’
“But I’m not there at training with them every day. I’m not seeing them in the gym or how they do in skills and defence sessions. There’s a myriad of things that make up a rugby player and the head coach has all this information at his disposal and makes the best call. He’s not trying to be unfair to anyone, he’s just trying to put his best team on the park to execute his game plan.
“Vern is a smart guy and I’m sure he’s got the balance right.”
Scott admits he was left sweating on his place in Cotter’s group after injury prematurely ended his club campaign with Edinburgh back in March.
“You are just never quite sure if you have made it or not so it is such a relief to get the call,” said the 24-year-old. “I felt excited and proud on Sunday when I did finally get the good news.
“I knew my time to impress was limited. I hadn’t played since the Six Nations and felt I hadn’t really done myself justice in the Six Nations at all, so I knew there was time pressure in the sense that I needed to train and play well.”
The Scots will round off their preparations for England 2015 with their final warm-up clash against France in Paris on Saturday.
Back-to-back wins over Italy have raised spirits in the Scottish camp after starting the year with six straight defeats.
But Scott knows they will face a Les Bleus side under pressure to sign off their build-up programme with a resounding home win at the Stade de France.
“To bring us back down to earth we have a really tough Test match this week,” he explained. “It’s a really tough place to go and we have not won there since 1999 so that has really sharpened our focus.
“[The French media] are expecting France to put in a good result on us. For me it will be a great indicator of where we are in terms of our development.”