Ecuador's Foreign Minister Francisco Carrion has described a renewed crop-spraying programme by Colombia along their border as a hostile act.
Ecuador says the herbicides cause damage to legal crops
Mr Carrion said that Ecuador was considering recalling its ambassador.
The drug-eradication programme is intended to target coca plantations controlled by drug traffickers and the left-wing guerrilla army, the Farc.
Ecuador claims the herbicides kill legal crops and cause health problems on the Ecuadoran side of the border.
The Colombian Foreign Minister, Maria Consuelo Araujo, has called for understanding from the Ecuadoran government.
Colombia stopped spraying a six-mile (10km) buffer zone in January after Ecuador complained that herbicides had drifted across the border and destroyed coffee and other legal crops.
But authorities in Colombia announced on Tuesday that they had resumed spraying due to an increase in coca production in the area.
"I understand Colombia's difficult situation. Without a doubt the situation is dangerous, but why should Ecuador have to pay for this situation?" Mr Carrion told local television.
"We can effectively recall or even completely withdraw our ambassador to Bogota, because this is a show of hostility toward Ecuador," he told the Ecuavisa network.
Meanwhile, Colombia's Vice President, Francisco Santos, told Reuters news agency that the government was willing to work with the Ecuadorean authorities.
"But we have to be implacable when fighting drug traffickers," he added.
Correspondents say this is the latest in a long list of diplomatic spats over Colombia's 40-year-old civil war, which has repeatedly spilled into Ecuador.