"I think the rule is rubbish," he said, speaking to reporters before Silverstone stewards imposed a 10-second post-race penalty on championship leader Nico Rosberg at the British Grand Prix.
The penalty demoted the German from second to third and cut his championship lead over team mate Lewis Hamilton, the race winner, to one point.
Red Bull's Max Verstappen moved up from third to second, his third podium of the season.
Despite the benefits to Red Bull of Rosberg's demotion, Horner said the rules that the driver "must drive the car alone and unaided" did not make a great deal of sense but had to be respected anyway.
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"The rules are the rules, and on two counts it sounds like instructions were given that breached that protocol," said the Briton.
"One was the switch change that was made and the second was the instruction how to drive the car with the seventh gear issue that they had."
Mercedes had told Rosberg what to do after his car had a gearbox problem five laps from the end.
Sunday was something of a test case for the rules, with Mercedes arguing that they had acted because Rosberg's car had a potentially terminal problem.
They have said they plan to appeal the stewards' decision.
Horner had warned that a light penalty risked setting a precedent that could open the floodgates.
"If it's just a five-second penalty or a reprimand, it's fair game for the rest of the year and there will be loads of messages that will take into account whether it's worth five seconds (added on) or not," he said.
"There's loads of information that we would like to give the drivers but we can't.
"The question going forward is 'are these rules right for Formula One?'," said Horner.
In Austria a week before Silverstone, questions were raised about the rules when Mexican Sergio Perez crashed after a brake failure that his Force India team had known was imminent but felt unable to warn him about.
FIA race director Charlie Whiting said then that relaxing the radio rule on safety grounds risked opening a loophole that teams might abuse.
(Reporting by Alan Baldwin, editing by Rex Gowar)
