La Liga president Javier Tebas said some authorities wanted to hide match-fixing and financial fair play issues.
An investigation has been launched into a clash between Levante and Real Zaragoza from last season, with players summoned in the match-fixing probe.
Tebas said the problems needed to be fought, not hidden.
"Regarding the match-fixing and financial fair play, from what I've seen in a year and a half as the president of La Liga, it has not been easy for the institutions to realise that this problem exists," he said.
"But in football, there are also some important institutions that want to hide the problem.
"Our integrity department in La Liga, for example, last weekend detected match-fixing activity in the third division. We detected the problem and communicated it to the responsible authority, but they chose to hide it.
"Probably because they don't want to recognise that this problem exists, even in the lower division."
Tebas said the governing body had to make sacrifices to help clubs, but believes they are paying their debts.
"There are two concepts for us," he said.
"It's not always acceptable to win in the pitch when match-fixing is about, and not everything is acceptable to be at a club which spends a lot of money to reach a target.
"In the last two years, a lot of things have changed but not that much regarding Real Madrid and Barcelona, it's impossible to compare them with others.
"We reported a loss of more than 100 millions of euros annually from the clubs three years ago just to get over 60 million in profits. This meant that clubs pay their debts."