The programme did not start at its scheduled time of one minute past 6pm, instead beginning at about 6.05pm.
To fill the four-minute gap, RTE rolled out ads for the Olympics and GAA.
When presenters Una O'Hagan and John Finnerty eventually came on air, confusion followed.
Ms O'Hagan read out the top headline on Tanaiste Eamon Gilmore revealing he had learned about the resignation of HSE chief Cathal Magee in the media.
However, Mr Finnerty then read out, word for word, the same headline, apparently without realising it.
As a result, the video footage in the second headline bore no relation to what he was saying.
In addition, when the news cut to a break at around 6.20pm, there was a black screen for about 30 seconds.
An RTE spokeswoman said the problem originated with the vision mixing desk - one of the most important pieces of equipment for the broadcast - which suffered a malfunction.
The mixing desk, which switches between cameras during the news, broke down just before Six One went on air.
"It was a major technical malfunction. While we were able to go straight to the emergency mixing desk, they took a few minutes to do it so we were on air later than normal," the spokeswoman said.
The mix-up with the headlines occurred as at that stage "everything was a bit under pressure", she added.
Ms O'Hagan and Mr Finnerty were standing in for RTE's regular Six One anchors Brian Dobson and Sharon Ni Bheolain.
Meanwhile, Pat Kenny has made a surprise return to a familiar slot as he hosted RTE's Prime Time.
The former Late Late Show star presented the station's flagship current affairs programme last night with Keelin Shanley.
It was a return to his roots for Mr Kenny who made his name as a current affairs broadcaster with Prime Time's predecessor Today Tonight.
He introduced an item on the conflict in Syria and this was followed by an interview with Al Jazeera journalist Rula Amin.
Mr Kenny then spoke with Nadim Shehadi, a Middle East analyst with think-tank Chatham House.
While Pat hosts the current affairs programme The Frontline, he spent most of the last 13 years on the Late Late Show.
He moved into light entertainment with Kenny Live before taking over from Gay Byrne on the Late Late in 1999.
Mr Kenny has been consistently praised over the years for his handling of political topics but the critics have been less kind about his showbiz interviews.
On one famous occasion, he introduced top US comic Jerry Seinfeld onto the Late Late as Jerry 'Seinfield'.