ScotRail Alliance chief Phil Verster has condemned the linking of his surprise departure with poor train performance as “totally wrong”.
It came as transport minister Humza Yousaf accused Scottish Labour leader Kezia Dugdale of a “bare-faced lie” in claiming punctuality had got worse since he ordered improvements.
ScotRail parent firm Abellio announced on Friday that Mr Verster was stepping down to lead a new rail project in England.
The news followed months of intense scrutiny for the train operator since it was ordered to implement an improvement plan after performance fell below acceptable levels.
The official measure of punctuality, the “moving annual average” [MAA] has improved to 90 per cent since then, but is still 1.1 percentage points below par.
Mr Verster is to become managing director of East West Rail - a new line between Oxford and Cambridge - after being approached last year.
Mr Verster told The Scotsman that media coverage linking his decision to quit with ScotRail’s performance was incorrect.
He said: “It’s totally wrong and looking to sensationalise my decision to take on a new challenge”.
Mr Verster said on Friday his new job was “great for me and my family”, which is understood to refer to his wife being keen to move back south.
They moved from York to Edinburgh after he becoming managing director of the ScotRail Alliance with Network Rail in 2015.
Nigel Harris, managing editor of RAIL magazine, said: “He’s not a quitter. I do not believe for a second he’s off with his tail between his legs.”
Mr Harris said Mr Verster would have been attracted by the rare and “genuinely exciting” new role at East West, where control of trains and tracks will be more integrated anywhere than since privatisation 20 years ago.
Scottish Conservatives transport spokesman Liam Kerr said: “Phil Verster may well be seeking a fresh challenge but events of the past week would strongly suggest there was friction between ScotRail management and the SNP Government.
“Humza Yousaf now needs to ensure this upheaval at the top level does not impact further on service delivery.
“Rail users will care little for who is at the helm of ScotRail - they simply want to see improvements and they want the trains to run on time.”
Scottish Labour transport spokesman Neil Bibby said: “Passengers will make up their own mind.
“The reality is the man ultimately in charge of the performance on Scotland’s railways is Humza Yousaf - who frequently tried to talk tough about ScotRail to deflect attention away from himself, and then produced a back of a fag packet fares plan which ScotRail admitted they had not costed.
“The buck clearly stops with the transport minister.
“With uncosted fares plans, poor performance, and the ScotRail boss moving on, Humza Yousaf must be feeling the pressure.”
Mr Yousaf tweeted that a claim by Ms Dugdale that “things have got even worse” since the improvement plan was a “bare-faced lie”.
He said: “Last period saw 6 per cent improvement on PPM [public performance measure] & improvement on contractual MAA + reduction in skip-stopping.”
However, Labour demanded an apology.
A spokesman said: “He agreed a ScotRail improvement plan when PPM was 90.7 per cent. The figure for the last four weeks is 89.7 per cent.
“It is simply unacceptable for a minister to falsely accuse an opposition leader of lying.”