Mr Varadkar, who is in Washington ahead of St Patrick’s Day celebrations, told the US Library of Congress Brexit had “undoubtedly changed the political weather”.
He said: “To me, Brexit is a threat to the Good Friday agreement simply because it threatens to drive a wedge between Britain and Ireland, between Northern Ireland and the Republic of Ireland, and potentially between the two communities in Northern Ireland.
“And that’s why we must do all that we can to make sure that those wedges, that that risk, does not become reality.”
The Irish Taoiseach’s comments come as Theresa May as repeatedly insists the UK is opposed to a hard border with Ireland.
And British ambassador Sir Kim Darroch, who was also at the event in Washington, told the audience: “The Prime Minister said in December last year that the UK remained committed to protecting north-south cooperation and to its guarantee of avoiding a hard border.
“Any future arrangements must be compatible with these overarching requirements.”
But the UK envoy was challenged by Colum Eastwood, the leader of the Social Democratic and Labour Party, Sinn Féin’s main nationalist rival, who said: “We are facing an enormous threat, one that we haven’t faced in a long, long time.
“It’s called Brexit. There are people who are using the Good Friday agreement, who are threatening to rip up the Good Friday agreement, just to make their negotiation with the European Union that little bit easier.”
The Irish PM also promised he did not have “a hidden agenda” for uniting the two Irelands under the guise of a Brexit threat.
Mr Varadkar said: “I know many are concerned, perhaps worried, perhaps even angry at some recent political developments and I want to recognise that recent statements and recent actions by Irish nationalists, including the Irish government, about Brexit have been seen by some as disrespectful and by others as intrusive or interfering.
“And if that was the case, I want to make very clear that that was certainly not our intention, and I want to repeat that we have no hidden agenda. We do not desire a border in the Irish sea any more than we want to see a border between Newry and Dundalk, or between Holyhead and Dublin.”
Last year Ireland’s foreign minister Simon Coveney said he would like to see a united Ireland in his “political lifetime”.
The Democratic Unionist Party (DUP) described the remark as “aggressive” and condemned “the megaphone diplomacy” of Dublin.
Brexit has raised fears of a return to a hard border between the Republic of Ireland and Northern Ireland reminiscent of the Troubles.
Officials from the UK and the EU are understood to be devising a plan to, in effect, keep Northern Ireland in the customs union and single market to avoid this outcome.
In her speech at Mansion House earlier this month Mrs May vowed to keep the UK united with no Irish border.
Mrs May declared it would be “unacceptable” to go back to a hard border or break-up the UK with a border down the Irish Sea.
The Prime Minister said: “Our departure from the EU causes very particular challenges for Northern Ireland, and for Ireland.
“It is not good enough to say ‘we won’t introduce a hard border, if the EU forces Ireland to do it, that’s down to them’.
“We chose to leave. We have a responsibility to help find a solution.
“But we can’t do it on our own. It is for all of us to work together.”