Bogota said Friday it was "worried" that tightened Ecuadorian entry requirements for Venezuelans fleeing an economic and political crisis would leave thousands stranded in Colombia.
Ecuador announced on Thursday that Venezuelans entering the country would need to show passports from Saturday onwards, a document many are not carrying.
And Peru followed suit on Friday, announcing an identical measure due to begin a week later.
"We're talking about 3,000 people a day, just Venezuelans" crossing into Ecuador alone from the border town of Rumichaca, said Colombia's migration director Christian Kruger.
"If they start gathering for a few days we're going to see a huge number of people" backed up on the Colombian side of the border crossing, he warned.
Kruger said he was "worried about the consequences" for Rumichaca because around half of the Venezuelans heading south through Colombia are carrying only ID cards rather than passports.
Ecuador and Peru are on Colombia's southern border. Venezuela is on its eastern flank.
"Asking for a passport isn't going to stop migration because they're leaving their country not out of choice but out of necessity," added Kruger.
Colombia will seek talks with Ecuador and Peru to discuss the problem, Kruger said, and is sending extra immigration personnel to saturated Rumichaca.
He also said he would push Colombia's southern neighbors to set up a joint fund and agree on a common migration strategy.
Kruger accused Venezuelan President Nicolas Maduro of practising a deliberate "policy of expulsion" towards his own people in order to reduce the country's population and "improve the distribution of resources."
Venezuela has been crippled by a four-year recession resulting in food and medicine shortages, the paralysis of public services including running water and electricity, and hyperinflation predicted to top out at one million percent this year.
The United Nations estimates that 2.3 million Venezuelans have fled the crisis looking for work and to escape poverty, while Colombia has given temporary residence to more than 800,000.
Many Venezuelans are aiming further afield to settle in Peru, Chile, Argentina or even Uruguay. Peru said 5,100 Venezuelans crossed into the country last Saturday, a record for a single day.
Before announcing its measure on Thursday, Ecuador had already declared a migration emergency last week.
Bogota says some 423,000 Venezuelans have passed through the border crossing at Rumichaca in this year alone.