Fine Gael Leader Enda Kenny opened the meeting by outlining his view on the situation and advising the party to draw a line under it and move on.
He said they should wish Mr Lee and his family well and leave it at that.
There were a number of speakers, with some criticism of the leader, as well as discussion of policy, communications and strategy.
The meeting broke briefly on two occasions for votes in the Dáil.
During one of those breaks, Michael Ring said there had been an 'open and frank discussion'.
Fine Gael Health Spokesman James Reilly said there were no mutterings about Mr Kenny himself, but perhaps more concern about backroom decisions that affect frontbenchers and backbenchers.
Dr Reilly said everyone at the meeting agreed that Mr Kenny was the man most likely to be Taoiseach after the next General Election.
Coveney criticises Lee's 'fanfare'
Earlier, Fine Gael's Simon Coveney said that Mr Lee chose to leave the party 'with great fanfare'.
According to Mr Coveney, Mr Lee used every possible media outlet to air his supposed grievances and to damage Fine Gael and Mr Kenny to the maximum extent possible.
'I don't forgive him for that,' Mr Coveney, who is the party's Spokesperson on Communications and Energy, said on RTÉ Radio's News at One.
He said it was regrettable that Mr Lee decided to 'abandon' Fine Gael and added that 'I gave him documents. I asked him to make comments, share his ideas. I didn't get anything back.'
Mr Coveney said that yesterday the Fine Gael front bench 'had a very robust and honest discussion' about the challenges for Mr Kenny and the party arising from Mr Lee's resignation.
'There were very hard questions asked of Enda, which he answered,' Mr Coveney said.
Mr Kenny's leadership style 'will appeal to people in time,' Mr Coveney said.
'That's the challenge for Enda. He needs to step up to that mark and if he can't achieve it well then there are the obvious consequences of that.'
