Speaking at a Washington defense summit, Clapper said it was "unlikely" that the Islamic State group had the capacity to carry out such an attack, but added "I wouldn't rule it out."
"We don't have any direct evidence of any terrorist involvement yet," he said.
The airline has said the Airbus 321 came down due to "external" factors, and that "no technical failures" could account for its apparent break-up in mid-air.
Investigators are examining all possible causes as they comb the remote crash site in the Sinai peninsula as part of an Egyptian-led probe into the disaster that also involves experts from Russia, Airbus, and Ireland, where the aircraft was registered.