The issue cropped up after Friday's opening match between Brazil and Bolivia saw empty spaces in the stands and the controversy grew on Monday.
The 65,601-capacity Morumbi stadium was filled with only 47,260 spectators, even though organisers had said the game was sold out.
Fans trying to buy tickets for Brazil games in advance faced difficulties and the Local Organising Committee (COL) said they had held some tickets back that later went unsold.
"We will perfect this to make the returns process quicker," the COL said in a statement.
The problem of poor sales was particularly evident on the second and third days of the tournament when three of the four games had attendances below 20,000.
Just 11,107 fans turned out for the match between Peru and Venezuela in Porto Alegre, and 13,611 watched Uruguay's 4-0 win over Ecuador in Belo Horizonte.
Only 19,162 people were in the 78,000-seat Maracana stadium to watch Qatar draw 2-2 with Paraguay.
"Of course, it's worrying because you want lots of people to see the best players in the world in action, because South American players are the best in the world," Alejandro Dominguez, president of the South American Football Confederation CONMEBOL, told reporters on Sunday.
"This is a country which lives for football and we would like to see more people participate. Some games have had many people, others unfortunately have not had so many.
"But, overall, the feeling is very positive and I think it's going to get better."
The COL said it would publish full details of sales on the tournament's website on Monday but the information was not available while they did not respond to requests for details on overall ticket sales.
Some fans blame the organisers for mishandling ticket sales while others blamed saturation with the ongoing edition of the Copa America being the third in five years.
Expensive tickets could also be a cause of poor attendance.
Cost of tickets for the Brazil-Bolivia game ranged from 190 reais to 590 reais (about $49-$152), while the lowest for most other games is 120 reais - still a considerable amount of money in the developing nation.
The 22 million reais (£4.5 million) from ticket sales for the opening match, even with partly empty stands, were the highest for a football match in Brazil, according to local media.
(Reporting by Andrew Downie; editing by Sudipto Ganguly)
