Leo Varadkar has accused Sinn Féin leader Mary Lou McDonald of undermining attempts to build an all-Ireland approach to tackle the Covid-19 pandemic.
At a Cabinet meeting on Tuesday, Mr Varadkar told ministers he believed that Ms McDonald is using the health crisis to forward her united Ireland agenda and said this risked damaging North-south relationships.
The Taoiseach's comments came after Ms McDonald suggested the virus would accelerate the cause of Irish unity because of the cross-border risk of the pandemic.
In an interview, she said the health emergency "dwarfs Brexit in terms of reflecting the danger of partition".
Her intervention sparked anger among unionists, who accused her of using a public health crisis to "create selfish political opportunity".
At the Cabinet meeting, Mr Varadkar criticised her comments during a debate with his ministers on the handling of the coronavirus crisis.
"The Taoiseach said Mary Lou McDonald's comments on Covid-19 being an 'accelerator' for Irish unity are unhelpful, and could undermine Ireland's efforts to build an all-Ireland consensus to deal with Covid-19," a source said.
"He said deputy McDonald is turning it into an issue of Green versus Orange, when it should always be treated as a public health issue."
Mr Varadkar and Ms McDonald also clashed on the issue during a teleconference call on the Covid pandemic for party leaders.
Sources said Ms McDonald raised concerns about how unionists were approaching the virus.
Mr Varadkar responded by referring to her comments on the coronavirus highlighting the need for a united Ireland.
He said it would be helpful if the pandemic was not turned into a "Green versus Orange" debate.
The Taoiseach's comments came after Ms McDonald wrote to him accusing the Government of raising expectations about the possibility of lifting the coronavirus lockdown restrictions.
The Dublin Central TD, who recently recovered from the virus, said the Government has caused "confusion and anxiety" by giving the public mixed messages.
She also said it was "critical" to take an all-Ireland approach to fighting the pandemic.
Last weekend, she told the 'Sunday Times' that Brexit has been an "accelerant in terms of the unity debate, because it was so obvious with the danger to the Border".
She added the virus showed how "vulnerable we are when we have two jurisdictions, two systems, on the island".
In response, Democratic Unionist Party (DUP) MP Sammy Wilson said the Sinn Féin leader should "dial down the rhetoric and political point-scoring".
"This crisis should not be exploited for political gain. Mary Lou McDonald's comments that coronavirus is an accelerator for a united Ireland are gratuitous," he said.
Ulster Unionist Party leader Steve Aiken also criticised the Sinn Féin leader's comments, saying the health crisis should not be politicised.
"It's utterly shameful that Mary Lou McDonald should seek to use this public health emergency to attempt to create selfish political opportunity in a crisis to advance Sinn Féin political ideology," Mr Aiken said.
Sinn Féin has also ramped up its political attacks on the Government's handling of the coronavirus pandemic.
Just as the public are becoming more restless with the Covid-19 lockdown, so too are members of the Cabinet which will decide tomorrow how long restrictions will last and how they might gradually be lifted.
Fianna Fáil and Fine Gael may have failed to commit to the Greens' demand for a 7pc reduction in annual emissions, but they offered plenty of firm commitments on the climate agenda to signal that the next government could be the greenest ever.