The newspaper Le Matin Dimanche said police turned out with screaming sirens and arrested the smokers after they were tipped off to the incident near the central city of Lucerne late last month.
The army had been giving a trial run to one of its seven drones, pilotless planes equipped with cameras and normally used to spy on enemy troops, when they observed the scene, the paper said.
The incident caused a Socialist member of parliament to make a protest statement, noting that citizens were not supposed to be spied on from the air without their knowledge.
In reply, Defence Minister Samuel Schmid said that the drones "are not made to spy on citizens", and did not have sufficiently precise cameras to identify an individual.
However he also defended the soldiers' action. "When one is serving one's country, one is also a citizen, and a citizen has a duty to denounce whatever seems abnormal," he told parliament, according to the report.
The paper said the soldiers had called the police after observing "a car and two individuals, apparently very agitated."
Although smoking cannabis is illegal in Switzerland, a survey published in 2000 found that six out of 10 people aged between 20 and 24 admitted to having partaken at least once.
The newspaper said the Swiss army had seven drones that were acquired from Israel in 1995. The craft fly at altitudes of between 1,000 and 3,000 feet (300 and 900 metres).