Knocke said the alert was issued "as a routine matter and out of an abundance of caution. There is no immediate threat to our homeland at this time".
Another government official said the threat had appeared on a website that called for Muslims to destroy American economic sites. The attacks were to be retaliation for the holding of Muslims at the US prison at Guantanamo Bay, Cuba, which houses prisoners accused of ties to jihadist groups.
The attacks were to be conducted in December, "until the infidel new year", the site said, according to a US government translation.
It called for attackers to use viruses that can penetrate internet sites and destroy data stored there.
The alert was issued by the US Computer Emergency Readiness Team.
The team, a partnership between private industry and a number of government agencies, is based at the homeland security department and warns websites about virus outbreaks and other internet attacks.
Spokespeople for the New York Stock Exchange and Nasdaq declined to comment on the cyber-terror threat.
A company called SFTI currently protects data transferred by all the major US stock markets. Each stock market also has its own firewalls, many of which were beefed up after the attacks