Gustavo Larrea, Ecuador's security minister, said the men were also probably plotting against other government officials.
Local media reported the men were found with photos of the presidential palace and maps of the nearby streets.
Larrea told Bogota-based radio Caracol that Ecuador was working with Colombia's police force to see if the suspects had a criminal record or if they were members of any armed or criminal group.
'Simply con men'
But Correa himself cast doubt on the plot.
"There is a high possibility that they are simply con men," he said on Thursday.
He said the men had demanded money for information on the plot.
Police must "continue to investigate, but we are not alarmed".
In an interview with a local television station on Thursday, Correa said that the plot was a "tip that we have been following for some time, but there is a strong probability they were just scam artists.
"We have dozens of cases like this every month".
Correa said last year that unidentified groups tried to buy rockets to kill him. But the government provided no evidence and no one was arrested over the accusations.
Correa cut off diplomatic relations with Colombia after a March 1
Colombian cross-border raid in pursuit of Revolutionary Armed Forces of Colombia (Farc) fighters into Ecuador's jungle.