Ponting said he would also have preferred the players to have had more input from Cricket Australia (CA) before the changes were instituted.
CA last month announced its domestic one-dayers would be split this season into two innings of 20 and 25 overs in a break from the single innings 50-over format.
Ponting said he was concerned that the new format would limit the preparation for some of the players currently outside the national team ahead of next February's World Cup in India, Sri Lanka and Bangladesh.
"We need to be playing as much 50-over cricket as we can with the World Cup just around the corner," he told reporters in Hobart.
"It'll be OK for the guys who are in the national side, we'll probably play another 12 or 13 one-dayers before the one-day World Cup comes around.
"(But) the guys on the fringe who are playing domestic cricket won't play any 50-over games really until that World Cup."
Ponting said the country's young spinners would particularly find it a difficult summer ahead.
The national skipper said the players should have had more input from CA before the changes were made.
"The players probably felt that they didn't have the input that they probably would have liked to have had," he said.
"I know there's been a lot of speculation about how it's going to be played, but it's up to the players now to play it as well as they can and make it a good spectacle."
The Australian Cricketers Association (ACA) has criticised the format, with chief executive Paul Marsh saying that the players had not been properly consulted.
"For the people that play and know the game better than anyone, this process has been difficult to comprehend and players are very disappointed," Marsh said at the time of CA announcement.
"Players are open to changes to any format of the game that can make the game better, but they don't believe the split innings format is the best solution."