The low-rating show was rumoured to be facing the axe after staff were summoned to a crisis meeting at Channel Ten's Sydney headquarters this morning.
The meeting was called last night to discuss the show's performance, Sydney's Daily Telegraph website reported.
Henry this morning said he was not aware of a meeting to discuss the future of the show, telling a Telegraph reporter he was more concerned with getting to work on time.
He later told Radio Live the show would continue, but there would be changes.
"Broadcaster Paul Henry has told Radio Live there will be changes to his Channel 10 breakfast show in Australia but it's not being axed," Radio Live said on Twitter.
Neither Radio Live nor media news site MediaSpy gave details of the changes.
A Channel Ten spokeswoman did not immediately return APNZ's call for comment.
The spokeswoman earlier refused to comment ahead of the meeting.
The Breakfast show has struggled to pick up viewers despite millions being invested in setting it up and revamping it.
It debuted with 51,000 viewers in February but viewership has since dropped off, with an average daily national audience of about 28,000 people.
It attracted just 1000 viewers on one day this month, and on one occasion there were no viewers at all in Melbourne for 15 minutes.
Ongoing tension between the co-hosts reportedly led to the departure of presenter Andrew Rochford last month.
The show's executive producer, Majella Wiemers, also quit. Former TVNZ staffer Sarah Bristow - who worked with Henry on TVNZ's Breakfast - took Ms Wiemers' place.
Last week, Channel Ten tried to douse the rumours about the demise of the show.
A network spokesman dismissed the chatter and called it the work of "naughty" people at other networks, a local newspaper reported.
