Australian Daniel Ricciardo finished second for Red Bull at the season-opener in Melbourne two weeks ago only to be disqualified for exceeding the fuel flow limit of 100kg per hour.
The team queried the accuracy of the sensor and have appealed, with a hearing scheduled for Paris on April 14.
Horner said he would talk with International Automobile Federation (FIA) technical delegate Charlie Whiting before Sunday's race in Sepang after Ricciardo's sensor failed and needed to be replaced on Friday.
The Briton added that he knew of other drivers who have experienced problems with the system.
"If we don't (get synchronised readings) we will find ourselves in an awkward situation, but one we will try to work with the FIA on, but we will find ourselves in the same dilemma as Melbourne," Horner said.
"We need a better way of measuring and monitoring the fuel flow, or say you get rid of it and you have 100kg for the race and that's it.
"Personally, I think it would be easier to get rid of it."
The FIA attempted to ease the confusion around the fuel flow system by holding a briefing to explain how it works and the regulations applied, suggesting they have no interest in modifying or removing it.
Fabrice Lom, the FIA's head of powertrain, said there were safety considerations.
"If you have no fuel flow limit, the fastest thing is to use a huge boost at the beginning of the straight and then lift off," he explained.
"There will be huge and very dangerous differences of speed (between cars) on the same lap, with a driving style that is not really F1."
Fuel flow sensors were not the only problem for Red Bull, however, with world champion Sebastian Vettel requiring a new electronic power control unit for Saturday qualifying and Sunday's race.
It will be the third time the German has had to replace a part of the power supply unit with only five changes permitted over the 19-race season before grid penalties are imposed.
The four-times champion finished Friday's second practice session third quickest with Ricciardo seventh to give the team hope that they can win points to get off the mark in Malaysia.
"I think we had a good day, obviously Friday timings are not the most important thing in the world but it's good to be up there and in range of the top guys," Vettel said after finishing 0.61 seconds behind Mercedes' Nico Rosberg.
"I think we had a decent day, not a completely smooth day for both of us, there are still some things to solve on the software side and the programming, but that's the way it is.
"I think we have to learn a lot but all in all, I'm quite happy."
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