The finance minister said journalism that makes people uncomfortable is "essential" and there should be "strong diversity" in Irish broadcasting.
Mr Donohoe was speaking exclusively to Dion Fanning for a new episode of Ireland Unfiltered.
This week, a new subscription news website called The Currency was launched by Ian Kehoe and Tom Lyons - the former Sunday Business Post editor and reporter who were unsuccessfully sued for defamation by Denis O'Brien earlier this year. It emerged on Wednesday that Communicorp had banned all reporters and contributors who work for The Currency from appearing on its radio stations. Communicorp is owned by Mr O'Brien, the billionaire businessman.
The ban means that none of the journalists and columnists writing for the new venture are allowed to appear on Newstalk, Today FM, Dublin's 98FM or Spin 103.8. In an email to staff, Communicorp said that the ban was because The Currency, which specialises in long-form business news, was "a competitor platform" for the radio stations.
Asked about his views on the ban, Mr Donohoe said: "I don't like to see it happen at all."
"I have great respect for the journalists and presenters in Communicorp. I'm on all of their shows all of the time, I think they're great. But for example, if I look at what The Currency are doing, what journalists like Ian Kehoe and Tom Lyons have done ... they make life uncomfortable for people like me and times and that's essential, it's just essential," Mr Donohoe said.
"Truth exists, and the search for truth and the debate around truth is just vital."
The minister said it was important to have "strong diversity in broadcasting here in Ireland." Asked if the ban was "a way for a radio station that has a licence to behave," Mr Donohoe said that the regulation of media "is correctly something that I play no role in, and that should never change." He said it was important to maintain a "gap" between politicians and editorial matters at broadcasters.
"Suffice it to say, I think all journalists should be afforded the platform for wherever they want to go. I look forward to seeing the day in which the journalists that we have just mentioned are on all broadcasters giving people like me a hard time, or analysing what we are doing," Mr Donohoe said.
Journalists working for The Irish Times have also been banned from appearing on Communicorp radio programmes since 2017, when Fintan O'Toole wrote that he would not appear on Newstalk again after George Hook suggested a rape victim was partly to blame for being sexually assaulted.
In the same interview, Mr Donohoe hinted that the 9% VAT rate for newspapers could be retained again in this year's budget, to protect democracy. In 2018, Mr Donohoe also kept the lower VAT rate for newspapers.
"And one of the reasons I decided not to put it up is I look at what has happened to the decline of local media in other democracies, and what that has meant for the ability of local events to be understood. And we don't want that to happen here," Mr Donohoe said.
Mr Donohoe's full interview on Ireland Unfiltered will be out on Tuesday.
