Double world champion Lewis Hamilton won last weekend's Italian Grand Prix with a 25-second margin over Ferrari's runner-up Sebastian Vettel.
In Friday's first practice, the Briton lapped more than a second and a half faster than Vettel -- whose car was the quickest after the Mercedes pair of Hamilton and Nico Rosberg.
"It (the Mercedes engine) looked quite frightening on Friday and then obviously they must have had some sort of issue with Rosberg because it looked like they wound the engines back a little bit," Horner said.
"But certainly the step that they made on Friday looked significant, quite worrying. I mean they are in a league of their own at the moment."
Rosberg had to revert to an engine that had done five grands prix for Sunday's race after a cooling problem. The unit then blew two laps from the end when he was in third place.
Horner, whose team's relationship with partners Renault now looks doomed despite one year remaining on the contract, said the race gave a glimpse of Mercedes' real speed when Hamilton was told to push hard at the end.
"We saw the kind of pace that Lewis had at the end there and it was pretty awesome, so I guess he was just managing the gap throughout the Grand Prix...they’re clearly some way up the road."
Red Bull have been linked to both Mercedes and Ferrari as they sound out other potential suppliers for 2016, with the latter having said as far back as June they would be willing to step in.
Mercedes have been considerably less keen, with Hamilton making clear his opposition, and reports after Monza indicated the German carmaker's board had ruled out supplying Red Bull.
Horner said he was still waiting to hear from Renault about their plans.
Renault are assessing their future in the sport, and whether to become more involved by buying into a team like struggling Lotus or quitting altogether.
"Obviously, time is starting to press on now, we’re now into September and everybody needs to know what are Renault plans for the future. So I would have thought within the next two weeks we should all know what Renault’s position is," Horner said.
(Editing by Ed Osmond)
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