Salvador said that Ecuador had "overwhelming evidence'' that the aerial spray had crossed the border and as a result "seriously affected" the health and livelihoods of many Ecuadoreans, as well as their crops and livestock.
Colombia rejects the charges and says the spraying is safe.
Ecuador says it is asking the world court to rule that Colombia has violated its sovereignty.
It also wants the court to order Colombia to halt spraying within 10km of the border and pay for the damage caused by the spraying.
The Colombian government, assisted by billions of dollars of US aid, often uses aerial herbicide spraying in a bid to destroy coca crop, used to make cocaine.
|Colombia is the world's top supplier of |
Colombia suspended spraying in response to Ecuador's complaints in 2005, but resumed in December 2006 after complaining that rebels from the Revolutionary Armed Forces of Colombia (Farc) had swarmed into the area.
Colombia is the world's top supplier of cocaine via its powerful drug cartels and the Farc has been accused of financing its war against the government with cocaine trafficking.
However, its neighbours allege that Colombia fails to stop violence from spilling over its borders.
Also on Monday, Colombia's government said that an Ecuadorean helicopter was intercepted by two Colombian Blackhawk helicopters on Sunday and forced to land near the frontier after its crew failed to answer attempts to make radio contact.
The aircraft, reportedly with two pilots and two passengers in Ecuadorean army uniforms, was ordered to the nearby Colombian port of
Later, however, it flew back over the border, the government was quoted by Reuters as saying.
"Once back in the air, the Ecuadorean helicopter, escorted by two Colombian helicopters, descended without warning, turned south and failed to obey instructions given by Colombian authorities," the presidential statement said.
Ecuadorean authorities were investigating the case, a defence ministry official said.
Tensions between Colombia and Ecuador remain high following Colombia's controversial cross-border raid on a Farc rebel camp in Ecuadorean territory on March 1 which left several Farc fighters dead, including one of the group's senior leaders, Raul Reyes.
The incident led to a furious diplomatic spat between Colombia and neighbouring Ecuador and Venezuela, who broke off diplomatic ties over the incident and sent troops to their Colombian borders.
Alvaro Uribe, the Colombian president, later apologised to Rafael Correa, the Ecuadorean president, over the incident at a regional summit.
But news that an Ecuadorean national had died in the raid re-ignited tensions.
Colombia still says that Ecuador has failed to combat Farc fighters on its territory.