Although President Reagan approved $20 million in emergency military aid for Honduras to repel a Nicaraguan border incursion last month, Honduras received only $410,000 worth of air transport and C-rations during the week-long fighting, according to congressional and administration officials.

The rest of the $19.6 million in military assistance has either arrived in Honduras since the emergency ended or is in the pipeline, a Defense Department spokesman said.

Rep. Edward J. Markey (D-Mass.) has complained that the aid delivered to Honduras after March 31 arrived after the emergency ended and is really "an end run around Congress" to provide ordinary military assistance in disguise.

"It's obvious the emergency is over, so the emergency aid should be over too," Markey said yesterday. "The president should not be permitted to use a temporary border incursion to circumvent established procedures for funding military aid to foreign countries."

A Defense Department spokesman, Lt. Col. Don Brownlee, said the administration viewed the emergency as a long-term one. "We see the threat as existing throughout 1986 and very conceivably beyond . . . the emergency has not gone away," he said. Markey's criticism is "one individual's judgment as to what constitutes an emergency."

Congress and the Gramm-Rudman-Hollings budget cuts reduced the administration's fiscal 1986 military aid request for Honduras from $87 million to $59.7 million. When large numbers of Nicaraguan Sandinista troops began moving across the border into Honduras on March 22, all the 1986 aid had been either obligated or committed, Brownlee said.

On March 24, Honduran President Jose Azcona Hoyo asked the United States for help, and the following day President Reagan notified Congress that he was requesting $20 million in emergency aid for Honduras under his special powers.

Reagan's written determination that an emergency existed said the aid would include "all air transport of Honduran troops as necessary, and other material assistance that may be necessary to repel the Sandinista forces and to prevent these attacks from recurring in the future."

The airlift began on March 26, the Sandinistas were reported leaving Honduras on March 27 and Reagan declared March 28 that they had been defeated. In a report requested by Markey, the Defense Department said that as of March 31, it had supplied Honduras with 15,000 "Meals Ready to Eat," or C-rations, and air transport for Honduran troops worth a total of $409,850.

Since then, Brownlee said, the Defense Department has supplied Honduras with more air transport to bring the troops back from the border, and with machine guns, ammunition, "a couple of landing craft," helicopter and aircraft parts, guns and mounts for helicopters, and Rockeye cluster bombs, the same kind that U.S. jets used on Libyan vessels in the Gulf of Sidra.

Other officials said pistols, antipersonnel and antiarmor bombs, and communications gear were also on the list. Brownlee confirmed that the administration is studying the possibility that the $20 million may ultimately include improved air-to-air missiles for Honduras' 12 aging Super Mystere jets, as well as ground-to-air defense missiles such as the hand-held Stinger, but that no decisions had been made.

Markey's definition of an emergency is "somewhat idealistic," Brownlee said, in that it does not address the possibility that similar situations might recur repeatedly. Regular U.S. military aid to the Hondurans is designed to modernize their armed forces and sustain their peacetime operations over a period of years "so that eventually they can defend themselves against threats in the area," he said.

But that program "did not consider the unique weapons for a specific land invasion that occurred," so the aid "essentially gave the capability to address that threat," now and in the future, Brownlee said.