Supporters with tickets for the June 7-July 7 showpiece were allowed to download and print them on Monday and a number of parents have since complained that seats have been allocated in such a way that they cannot sit with their children.
The tournament organisers initially released a statement saying they could not change seat allocations except for parents with children under the age of 18 who were not seated together.
In a subsequent statement organisers said less than 1% of fans with tickets for the semi-finals and final were facing seat-allocation issues.
"The previous tweets regarding FIFA Women's World Cup tickets allocation were published without a full understanding of the situation and we apologise for that," organisers said in a statement on Twitter.
"The issues were faced by less than 1% of fans requesting tickets for the semi-finals and the final. FIFA and the local organising committee are confident the problems will be solved and fans will be able to enjoy the matches as they envisaged."
The assurances did not calm supporters on social media, who suggested the problem was far more widespread and demanded organisers resolve the issue.
Twitter user Gareth James complained he would have to sit separately from his two daughters and would not attend the game if their seats were not reallocated. "How will (the problems) be solved? Me and my daughters aged 11 and 13 have tickets that are not together, so will not be able to attend," he tweeted.
A fan named Mike Swanson said he had been crushed to discover that his family of five, which includes three children, would be spread over three different rows.
"This was to be a family trip and we can't even sit together as a family," he said in a tweet. "What a disappointment. Not a happy customer."
FIFA released a statement later on Tuesday saying they were still working on a solution. "FIFA and the local organising committee are... doing everything they can to ensure that families will always be seated together at each and every match," the statement said.
"Of the 1.3 million tickets on sale for the tournament it is estimated that not having side-by-side seats will affect only a very small number of fans."
The women's World Cup semi-finals and final will be held in Lyon.
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