On Thursday, Howard presented Flannnery with the annual Australian of the Year award.
"We've lost a decade [to] inaction and we've held the world back really from addressing this issue because we haven't been part of Kyoto," Flannery said.
"So we need to move doubly swiftly now and this year is the year we need to see that action."
Flannery said he welcomed plans announced by the Howard government earlier this week to spend billions of dollars to protect Australia's dwindling water supplies.
But he said that was just part of the environmental jigsaw puzzle.
Howard maintained until late last year that there was little evidence for global warming.
Although Howard now admits "climate change is occurring", he told Australian radio he remained unconvinced of Flannery's arguments about the need to back Kyoto.
"We've got to remember that many of the international rules in this whole area, particularly Kyoto, have been written by Europeans to suit Europeans with scant regard for the interests of countries such as Australia," he said.