A department advisory said al Qaeda was in the late stages of planning an attack on the consulate using a small fixed-wing aircraft or helicopter.
Such a plot, along with one uncovered last year in which al Qaeda hoped to fly a small plane into a U.S. warship in the Persian Gulf, demonstrated a "fixation" on using aircraft in attacks, the advisory said.
The warning was issued Thursday to U.S. pilots and airport managers as part of a broader bulletin urging vigilance to guard against similar attacks in America.
A U.S. law enforcement official, speaking on condition of anonymity, said a plot against the consulate was uncovered with the arrests earlier this week in Karachi of Waleed bin Attash and five other alleged al Qaeda members. About 300 pounds (135 kilograms) of explosives and a cache of weapons were seized.
Attash is believed to have played a leading role in planning for the Sept. 11 attacks and the bombing of the USS Cole in Yemen.
Homeland Security officials say there is no specific evidence about an attack using small aircraft in the United States. But the advisory says al Qaeda could try to use such planes because they are easily available and require less pilot skill than large jets.
Security procedures also are less rigorous for small aircraft; there would be no need to attempt to control a large group of passengers and a credit card could be used to rent such a plane, the advisory said.
It said: "Reliable information obtained last year indicated al Qaeda might use experienced, non-Arab pilots to rent three or four light aircraft under the guise of flying lessons."
Pilots and airport officials and workers were urged to be extra alert for suspicious people and activity, aircraft with unusual modifications or people loading unusual cargo onto an aircraft. Vigilance should also be maintained in checking identification, verifying baggage and cargo and watching for "persons who appear to be under stress or under the control of other persons."
The Aircraft Owners and Pilots Association, which represents general aviation interests, issued a statement Friday saying it supports greater vigilance but questioning "the sweeping generalizations in this DHS advisory that aren't necessarily accurate," said Phil Boyer, the group's president.
Boyer took issue with a section of the advisory saying that a small plane loaded with explosives could do as much damage as a medium-sized truck bomb. Such a plane, he said, could carry only a few hundred pounds (a couple hundred kilograms). A truck similar to the one used in the 1993 World Trade Center bombing carried 1,500 pounds.
An even stronger denunciation of the advisory came Friday from the National Air Transportation Association, which represents aviation businesses. It said the advisory presented "an irresponsible picture" of the charter and general aviation industry.
In March, the Transportation Security Administration joined with the AOPA to send brochures to 200,000 pilots urging them to watch for suspicious behavior. Posters also were sent to airports and flight schools.
There are about 18,000 private landing sites in the United States, many with little or no security. After the Sept. 11 terrorist attacks, the government grounded thousands of crop-dusters amid fears the planes could be used in an airborne chemical or biological attack.
Restrictions also have been established for private planes around nuclear power plants, military installations and in Washington and other cities.