In conjunction with Mercedes, Pirelli conducted a tyre test at Barcelona's Circuit de Catalunya following the Spanish Grand Prix.
Under the sporting regulations in-season testing is banned. However, it is understood in Pirelli's tyre-supply contract it is allowed private tests with individual teams should circumstances require.
With Pirelli due to slightly alter the structure of its rubber on safety grounds from next month's Canadian Grand Prix, and with tyres for 2014 due to change considerably given the new engine regulations, the Italian manufacturer felt it crucial the tyres were tested.
At present Red Bull and Ferrari are considering a protest, and are in discussions with motor sport's world governing body, the FIA, about the matter.
Horner, who only discovered what had taken place last night, is far from happy.
"First of all we need to deal with it through the proper channels, and that's what we'll look at doing," said Horner.
"There is confusion between what is contractually permissible and what a team is allowed to do in the sporting regs.
"It's a situation we need clarification on, and our position is we are going to request that clarification.
"I can understand Pirelli wanting to test the tyres, they've obviously got issues with the tyres.
"What's disappointing is it's been done in not a transparent manner, that a three-day test has taken place with a current car running on tyres that are going to be used at the next grand prix.
"Irrelevant of what you call it, that's testing."
Asked whether it had helped Mercedes who start on Sunday's race with Nico Rosberg and Lewis Hamilton out in front, Horner added: "Well they've both cars on the front row of the grid, so it's not hurt."
Pirelli motorsport director Paul Hembery, however, claims the test was above board and does not believe Mercedes gained any advantage.
"It's completely regular in that we are allowed to do a 1000-kilometre tyre test with any team," said Hembery.
"In the World Rally Championship contract it's exactly the same. We can do it with a representative car.
"We've done it before with another team, and we've asked another team to do some work as well.
"In reality, we were looking at next year's solutions and trying a variety of different things.
"Mercedes haven't a clue what on earth we were testing in reality."
Asked about the prospect of Mercedes gaining the upper hand, Hembery added: "Absolutely not, no, because it's no relevance to what's happening here.
"The bottom line is we've been trying to find a way to test."
Regarding whether it was with this year's tyres or those for next year, Hembery said: "Ninety per cent next year. We changed at the last minute."
There was no comment from the FIA when contacted by Press Association Sport.
Niki Lauda, the non-executive chairman of Mercedes GP, has confirmed the team were given permission by the FIA to conduct the test after seeking clarification.
Speaking to SkySportsF1, three-times F1 world champion Lauda said: "It is very simple, we asked the FIA 'Are we allowed to do this?'
"The FIA confirmed it and said 'yes', so therefore we did the test. I think other teams have been asked too.
"There was one team that tested earlier. These tests can always come in cases of emergency, so Mercedes did absolutely nothing wrong.
"We asked the right people for permission and we got it."