Pat Bourne, who is based at Ireland's consulate general in Edinburgh, said the acts of anti-Irishness reported since he took up the position were "disturbing" and that the "appalling" legacy of sectarianism in Scotland must be purged.
But the Scottish anti-sectarianism charity Nil By Mouth said it was wrong to say sectarianism in Scotland "is unique to any one community or religious group".
Mr Bourne said: "The lingering and continuing legacy of sectarianism and anti-Irishness in Scotland is a serious issue. I would not want to overstate the scale of that, or the frequency in which that comes up, but it is an issue and the Irish community in Britain and Scotland will have noted some of the incidents over the past few months."
Mr Bourne, who became consul general four months ago, said he was concerned to read of the British soldiers who were filmed singing allegedly sectarian songs at an armed forces day at Ibrox stadium in Glasgow in September last year.
A police and Army probe was launched over "concerns" raised after 400 personnel from all three forces were invited to Ibrox for the game between Rangers and Stenhousemuir.
Despite evidence that four soldiers had posed with a scarf with a sectarian slogan on it, last month it emerged that no formal Army disciplinary or criminal action had been brought.
There was outrage when a video emerged from the game, which appeared to show military personnel dancing and applauding in front of singing fans before Rangers went on to win 8-0. Senior personnel from the Armed Forces looked on from the directors' box.
"The appalling case of British soldiers seemingly engaging in anti-Irish sectarian singing and chanting on video was quite disturbing," Mr Bourne said.
"And the fact that no action seems to have been taken is quite disappointing."
In January it emerged that a Glasgow private hire driver was under investigation for allegedly refusing to allow Irish visitors to speak their native tongue in his car. The man was accused of offloading the passengers at the side of the road at 2am after they objected to his demand that they stop speaking in Irish Gaelic.
Mr Bourne described that incident as "quite disturbing".
He said he now wants to tackle the sectarianism issue during his four-year term in Scotland.
"I wouldn't draw links between these events or say there is a pattern here, but even a single incident like this is just not acceptable in a modern democratic country that serves human rights, standards and the norms in the 21st century," he said.
"We should not be complacent or satisfied until sectarianism is completely consigned to history and wiped out altogether," he added.
"That's one area I really would like to make progress on in the years that I am here."
Nil by Mouth campaign director Dave Scott said: "While the consul will obviously have an interest in the experiences of the Irish community in Scotland we should avoid falling into the trap of thinking sectarianism in this country is unique to any one community or religious group.
"The evidence tells us this is not the case and we should never forget that 100% of victims of sectarianism are first and foremost human beings."
A new campaign aimed at giving the victims of hate crime the courage to report attacks was launched by the Scottish Government earlier this week.
The move followed figures showing there were more than 4000 charges of racially aggravated hate crime last year.
There was also said to have been a significant rise in reported charges for incidents related to someone's religion, sexual orientation or disability in 2012-13.
A Scottish Government spokesman said: "We will not tolerate any form of racism or sectarianism regardless of who it is perpetrated against.
"We believe that our communities need to be at the heart of our work to tackle sectarianism. That's why the Scottish Government is investing £9 million over three years in a range of projects aimed at challenging and changing attitudes at local level through education, football, youth work and community mediation."