The suspension, however, is on hold for five days giving Quindio the chance to settle their debts and avoid missing matches in the round-robin phase of the Apertura championship.
"If Deportes Quindio gets up to date with its labour and social security obligations towards its sportsmen ... this suspension measure will be lifted immediately," Coldeportes (Colombian Sports Institute) said on its website.
The Colombian Football Federation (FCF) and the league, Dimayor, criticised the sanction at a meeting on Wednesday.
The sanction could also draw the wrath of world governing body FIFA who have previously threatened to suspend national governing bodies for government interference in football matters.
Dimayor president Ramon Jesurun said he and FCF head Luis Bedoya would meet with Coldeportes chief Jairo Clopastofsky to "show there was abuse of authority and violation of due process," the daily El Tiempo reported.
Coldeportes, which has been investigating the running of Colombia's clubs, said Quindio can play their next match in the championship against Real Cartagena at the weekend before the ban will take effect.
Failure to pay on time is endemic in Colombian professional football with several first and second division clubs in debt to their players.
Quindio took their protest over three months' unpaid wages a step further than other clubs by refusing to travel to Bogota on Sunday for the match against Millonarios.
Club owner Hernando Angel sent his under-20 amateur team Boca Juniors del Valle in their place and they were beaten 5-0.
Thank you for reading 5 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1