Ramon Jesurun, president of the league's governing body Dimayor, said that club finances had plummeted since the country had largely managed to eradicate drugs money from the sport.
"In Colombia, drug trafficking spread into all economic, social, religious activities, into journalism, everything, including football," Jesurun told Reuters in an interview.
"Today, fortunately, that's been almost totally eradicated in Colombia, in football, too," he said on a visit to Paraguay for the South American Football Confederation's congress.
"That might explain the poverty of the clubs today. If the clubs didn't have the effects of the narcotics traffickers, we wouldn't have the structural weakness from the economic point of view that we have today and are trying to fix."
Clubs in the two professional divisions are often behind with players' wages and social security contributions, sparking industrial action and the threat of government-imposed bans in recent weeks.
Top-flight club Deportes Quindio's players refused to travel to a match in Bogota last month over unpaid wages, sending a youth team that were hammered 5-0 by Millonarios.
The government's sports regulator Coldeportes has looked to impose suspensions on clubs over unpaid wages, but Jesurun said the government needed to do more to help those that were operating under a vulnerable business structure.
"Most stadiums in Colombia belong to the state and the infrastructure and logistics of staging a match is handled by the government of each city at very high tax costs that make for very big investment (by clubs) to organise a match," Jesurun said.
"We want to be seen as an economic sector like any other and the other economic sectors get help when they enter into crisis.
"We are asking for the same thing, we're as important as them and perhaps even more so because we're the ones who generate the most important recreation and entertainment for a country that today has nearly 50 million inhabitants."
Colombia's soccer chiefs and government officials will hold a summit on Thursday in an attempt to begin curing the many ills afflicting the domestic game, including hooligan violence which has soared in and around stadiums in recent years.
Jesurun said a draft Sports Law aimed at improving financial matters and combatting violence had made its way through parliament and was awaiting presidential passage, which could also come on Thursday.
"There has been a big increase in (football-related) violence in Colombia," the 58-year-old Jesurun said.
"We believe the hard-core fan groups are no longer supporters but delinquents disguised in team colours which is quite different, but we're trying from a legislative point of view to control it so those delinquents are given severe and hard penalties.
"Minors are strongly protected in Colombia as in the majority of countries and generally the so-called leaders of the gangs use minors because they know they have immunity, but that's where we're trying with the government and our legislators to radically change that."
