Ms Dugdale dramatically quit the post of Scottish Labour leader in August, with leftwinger Richard Leonard and the more moderate MSP Anas Sarwar now competing for the job.
Mr Rowley, who had been Ms Dugdale’s deputy, was made interim leader of the party - and as such said he would be neutral in the leadership contest.
However a recording emerged from Labour’s UK conference in Brighton of him backing Mr Leonard, a former trade union organiser who was elected to Holyrood in 2016.
Former MP Gemma Doyle said afterwards it was “troubling” Ms Dugdale did not appear to have been able to rely on her deputy for support.
Ms Doyle told BBC Radio Scotland’s Good Morning Scotland programme: “I think there has been a problem since Kez and Alex took over as leader and deputy, because I think as Kez herself has said there has been undermining of Kez by Alex for some time now.
“And I really think he needs to consider his position. You can’t be saying publicly you’re going to be neutral then privately... this wasn’t even a discussion between himself and a close adviser or anything like that that was overheard, he seems to have fairly openly been discussing who he thought was the best person to lead the Scottish Labour Party.”
Ms Doyle had been elected as the Labour MP for West Dunbartonshire in 2010, but lost the seat five years later when the SNP completed a rout of the Scottish seats at Westminster.
She said there was “quite a spat now in the Scottish Labour Party” and added: “Loyalties run very deep in the Scottish Labour Party and grudges run even deeper, I think it’s fair to say.”
The former MP added: “As a leader you should be able to expect loyalty and support from your deputy, particularly in Scottish politics which is quite a small world, there’s not a huge number of Labour MSPs.
“I wish there were more but they are a small group, and for Kez not to have been able to feel that her deputy was on her side is really quite troubling.”
She spoke out after the recording, obtained by The Sun, of a private conversation in which Mr Rowley, the MSP for Mid Scotland and Fife, told a student at the Labour conference: “Although I’m neutral in the leadership I also believe that Richard Leonard has everything that we need to win in 2021. I really do.”
He added that while left wing factions within the party were not “putting any pressure” on Ms Dugdale to go, they “didn’t believe Kezia would be there in 2021”.
Ms Dugdale only gave Mr Rowley 10 minutes notice she was stepping down before the decision was made public, saying people “would be right” if they though that “speaks to a lot of internal problems in the Labour Party”.
Labour MSP Jackie Baillie, a long-time ally of Ms Dugdale, said afterwards “what is most concerning is the revelations about a plot against Kezia Dugdale”
Last week Mr Rowley was forced to deny he had deliberately set Mr Sarwar up during First Minister’s Questions at Holyrood, after his reference to ‘’millionaires’’ allowed Nicola Sturgeon to attack the leadership candidate for his personal wealth.
DOWNLOAD THE SCOTSMAN APP ON ITUNES OR GOOGLE PLAY