According to Marsh, players are not happy with the 45-over split innings format which was approved for trial during this summer's domestic season by Cricket Australia yesterday.
The new format will be used across all 31 matches in the domestic competition.
"The decision by CA to trial the split innings format in this year's domestic one-day event was made before collective player input was even sought," Marsh was quoted as saying by 'The Australian Associated Press'.
"For the people that play and know the game better than anyone, this process has been difficult to comprehend and players are very disappointed," he said.
Cricket Australia was quick to react with its CEO James Sutherland saying that the changes are bound to create "understandable discomfort or trepidation" but players "are not the only stakeholders" in the game.
"In talking to stakeholders, the ultimate thing was the tournament should be played over the course of a whole year," said Sutherland.
"To do a proper trial and to ensure the public fully understand the way it's played, certainly that was the feedback from fans and other stakeholders. There is no doubt there are issues for individual players and preparation for the World Cup coming up," he added.
Sutherland rejected apprehensions that the format would adversely impact the cricketers' preparation for the 2011 World Cup in the sub-continent.
"Players who maybe won't get as much one-day cricket in preparation for the World Cup in the traditional form, will work with selectors to see if any players under the microscope they can form a position on them," Sutherland said.
The new format will have two innings, the first of 20 overs and the second of 25 overs.
Bowlers will be able to bowl a maximum of 12 overs instead of 10 and pacemen will be allowed to send down two bouncers per over rather than the current one.
The format was approved by the board after being given the go-ahead by CA's playing conditions committee which includes former players Mark Taylor, Matthew Hayden, Greg Chappell, Shane Warne, Marsh and CA chairman Jack Clarke.
Marsh said players were against changes in the game but they did not consider split innings format a solution.
"Players are open to changes to any format of the game that can make the game better," he said.
"They acknowledge that the one-day format has had its recent challenges and as a collective they want to help those running the game find the best solution.
"However, the players don't believe the split innings format is the best solution," he added.