At last month's board meeting in Edinburgh, the International Cricket Council announced the main part of the tournament in southern Africa will contain a dozen teams split into two groups of six.
There will still be 14 participants, but the tournament is slated to start with a preliminary round involving the three lowest-ranked qualifiers, with only one team progressing to the group stage.
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A qualifying tournament will be held from February 22 to March 23 next year, with the winner going through to the main tournament and the second, third and fourth placed teams entering the first round.
In a joint statement, Cricket Scotland and the Royal Dutch Cricket Association (KNCB) said they were "deeply disappointed" by the ICC's decision, announced less than 18 months before the tournament is due to start.
The statement said: "At a time when cricket is seeking to expand its reach, attract new audiences and strengthen its position on the international sporting landscape, reducing meaningful opportunities for emerging nations sends entirely the wrong message.
"We have significant concerns about both the impact of these changes and the process through which they have been introduced.
"The changes risk weakening the integrity and credibility of international cricket, and only highlight the importance of strong governance, transparent decision-making and effective engagement with members."
Scotland and the Netherlands are currently 13th and 14th respectively in the men's ODI rankings.
Monday's statement follows the World Cricketers' Association expressing its concerns about the tournament revamp although Cricket Scotland and the KNCB say they are "fully committed to working constructively with the ICC and fellow members to strengthen the global game".
However, the statement added: "Following the announcement of the changes, Cricket Scotland, the KNCB and other associate members met twice with the ICC, seeking official written communication on the changes and greater clarity around the processes involved.
"We also requested positive action to strengthen future operational decision-making and an invitation to bilateral planning meetings with full members.
"Since the second meeting more than two weeks ago, there has been no further response from the ICC, which is disappointing and disrespectful given the significance of the issues raised."
Sky Sports News has contacted the ICC for comment.
