Denis Naughten had four private dinners with the only bidder for the national broadband plan, the Taoiseach has said.
Speaking in the Dail this afternoon, Mr Varadkar said that he asked Mr Naughten to resign last night upon learning of the meetings with businessman David McCourt.
Mr Naughten tendered his resignation today as Minister for Communications.
The Taoiseach said he left himself open to allegations of a conflict of interest in how he handled the awarding of the contract the broadband plan, and that his actions left him with no choice but to seek his resignation.
Richard Bruton has been appointed as Communications Minister "on a temporary basis", Mr Varadkar said.
In a statement issued by the Taoiseach, he said that he had "no doubt that he [Denis Naughten's] intentions were honourable at all points" during his meetings with Mr McCourt.
"But I do believe he left himself open to allegations of a conflict of interest and an inappropriate relationship with Mc McCourt which could have in turn brought the process into question, thus potentially jeopardising the project in its entirety.
"I deeply regret that these events have happened. But I believe in resigning, Denis has acted in the public interest. I am determined to see the National Broadband Plan through to completion.
"Sometimes there are days when I have to make decisions that may cause deep personal distress to others but are necessary for the good of the country. Today is one of those days.
"I have known Denis for over twenty years and we were in Young Fine Gael together and I have had nothing but respect for him as a person and a politician. I know today is a difficult day for Denis and those close to him. However, my job as Taoiseach must always be to put the public interest first."
Earlier: Denis Naughten resigns as Communications Minister after broadband controversy
Communications Minister Denis Naughten has resigned from cabinet over revelations he met three times with the only bidder still in the national broadband plan process.
In a shock statement to the Dáil this afternoon, Mr Naughten said bluntly "I've given the Taoiseach my resignation", saying "it is clear the Taoiseach does not have confidence in me".
On Wednesday, it emerged Mr Naughten held a hugely controversial and previously unknown June 28 meeting with billionaire Irish-American businessman David McCourt.
In addition, it also emerged Mr Naughten "facilitated" and paid for a €37 Leinster House lunch for Mr McCourt and his daughter on April 18, although he did not attend.
The meetings followed a third meeting with Mr McCourt in New York in July.
On Wednesday, Mr Naughten responded to questions from the Irish Examiner over whether he will resign by saying he has done "nothing wrong".
However, 24 hours later, he told the Dáil this afternoon he is quitting cabinet.
Mr Naughten said he met Mr Varadkar last night to offer to move aside on the national broadband plan and give his responsibility on the matter to junior minister Sean Kyne.
He said he also offered to instigate a review of his role in the matter.
However, after saying Mr Varadkar responded by telling Mr Naughten he needed to "reflect on my position", Mr Naughten said "it is clear the Taoiseach does not have confidence in me".
"I'm now left in that impossible stark position a politician never wants to be in. Do I make the decision to resign or wait for the decision to be made for me. It's more about optics than fibre optics," he said, before adding to shock in the Dáil:
"I've given the Taoiseach my resignation."
The decision by Mr Naughten to quit the cabinet will intensify fears of a potential general election, although it remains unclear at this stage if he will continue to support the Government.
In addition, the decision is believed to have caught both Taoiseach Leo Varadkar and other senior cabinet officials off-guard, as Mr Varadkar and Tánaiste Simon Coveney were not present in the Dáil when Mr Naughten stepped down.
Responding to Mr Naughten's shock resignation, a number of Fianna Fáil TDs including Timmy Dooley, Eugene Murphy and others turned their targets to Taoiseach Leo Varadkar, who they insisted now has questions to answer.
In particular, Mr Murphy said:
"One person is to blame, the Taoiseach. He may have thrown Denis Naughten under the bus, but I would remind the Taoiseach the bus is still rolling down the road and he is wandering all over that road. This could be the rock he falls on."
Green party leader Eamon Ryan repeated the question, before adding bluntly: "Do we have a Government? That's the sort of question we have this afternoon... I think the future of this Government hangs in the balance this afternoon, that's the real story."
Similarly, Independent TD Thomas Pringle said: "The chief whip is running around trying to rally members now, when everyone else seems to have fecked off and not aware of what happening."
Independent TD Michael Fitzmaurice said: "It's nearly like down the country when someone dies, everyone says how great you were when you're gone."