He said the Mexican presidential poll, which a controversial leftist mayor is favoured to win, bodes ill for economic reforms sought by President Vicente Fox.
Interior Minister Santiago Creel accused Goss of interfering in Mexico's domestic politics.
"As you know, the CIA often gets it wrong," the minister told journalists on Thursday.
"I reject the interference in Mexicans' internal affairs which the CIA has no reason to be commenting on," said Creel, himself a possible candidate in the presidential race.
Political tension has risen in recent weeks in Mexico. The leftist mayor of Mexico City, Andres Manuel Lopez Obrador, has called for street protests to persuade Congress not to block his candidacy.