Merkel looked on apparently amused as the about 40-centimetre (16-inch) wide device, fitted with a camera, dropped down on the podium just metres away from her at the Christian Democratic Union (CDU) event Sunday in the eastern city of Dresden.
A week before Merkel seeks a third term in general elections, the internet-freedom Pirates, who campaign for greater transparency in politics, said they wanted to take aim at the government's stance on drones.
They had sought to convey to Merkel and Defence Minister Thomas de Maiziere, on the podium with her, "how it feels to suddenly yourself be observed by a drone", the party's deputy chairman Markus Barenhoff said in a statement.
"For us, the use of drones within the EU's security framework is the expression of a disastrous trend," he added.
It was also a protest against a scrapped spy drone deal which had already swallowed more than €500 million before being axed earlier in the year, said the statement, posted on the party's website.
An unidentified Pirate party member, who operated the drone, said it was solely aimed at videoing Merkel and other CDU politicians.
After police forced him to ground it, he conducted an emergency landing "in the area in front of the stage in order not to endanger anyone", resulting in a bumpy landing, he added.
A 23-year-old man was temporarily detained in connection with the incident.
Government spokesman Steffen Seibert declined to comment, beyond telling reporters that Merkel "has confidence, as she always does, that what's necessary for her security is done."
An interior ministry spokesman told the same news briefing that the federal police, responsible for Merkel's personal security, had "taken note of the incident and will draw its conclusions from it".
Last month media reports that a 24-year-old man had managed to board a government jet used by Merkel while it was parked in the military section of Cologne airport raised security questions.
The bodybuilder was reported to have been carrying marijuana and ecstasy pills when he climbed into the Airbus 319 where he sprayed extinguisher foam, pressed cockpit buttons and was dressed in just his underpants.
The incident reportedly happened on a July evening while Merkel attended a performance of "The Flying Dutchman" at the Bayreuth Wagner opera festival.