The Reagan administration has decided to give the noncommunist Cambodian resistance $3.5 million in nonlethal aid to be administered through Thailand, administration sources said yesterday.

The aid, they said, would be for short-term support of the two main noncommunist groups fighting the Vietnamese occupation of Cambodia. The aid would include medicine, shortwave radios and batteries as well as paramedical and civilian training, State Department sources said.

Although the guerrillas reportedly have received funding channeled by the CIA through Thailand, the $3.5 million would be the first direct and open aid to the noncommunist groups. The sources said it is intended to demonstrate support for the noncommunists, who are allied with the communist Khmer Rouge in a loose coalition against the Vietnamese occupying Cambodia.

Congress passed legislation in December giving the administration the discretion to provide between $1.5 million and $5 million in aid. But shortly after the legislation passed, a quarrel within the leadership of the larger group, the Khmer People's National Liberation Front, broke into the open. A dissident faction formed its own organization to challenge the leadership of front leader Son Sann.

This disarray caused noncommunist countries in the region to question the ability of the noncommunist guerrillas to make effective use of U.S. aid at a time when the Khmer Rouge appear to be gaining strength inside Cambodia. Thai officials were reported to be so displeased with the latest squabbling that they threatened to stop aiding Son Sann's front, Asian diplomats said.

But that squabbling did not figure into the administration's limited allotment of aid, the sources said. "Things are going to be resolved" in the front, said one State Department official. "The folks who are in charge of the military side of things are still in charge."

The administration initially had set aside only $1.5 million for the guerrillas, but after other administration officials pointed out that the amount would not be in keeping with the administration's public posture on aiding the noncommunist rebels, the amount was increased to $3.5 million, sources said.

Officials said the nature of the aid had changed from an emphasis on training for the long term to one on the resistance's more immediate needs.