Christian Horner fears teams could be penalised by the FIA's fuel flow sensors, which would ultimately decide the outcome of grands prix.
This season, for the first time, the Formula One teams are limited to 100kgs of fuel per grand prix with a maximum fuel flow rate of 100kg/h.
The rate is measured by a fuel flow sensor provided by the FIA.
However, after just one grand prix, the technology has already been questioned.
Several teams found the sensors to be inaccurate during the opening race weekend in Australia prompting Red Bull to ignore them and rely on their own data.
This resulted in Daniel Ricciardo being excluded from the Australian GP results as, according to the FIA sensor, his RB10 had consistently exceeded the fuel flow rate.
And unless a reliable method of measuring the rate is found, Horner fears teams could be penalised while others benefit from a better reading.
"We have got to find a better way - especially when the margins are so fine and the knock-on in performance is so significant," the Red Bull team boss told Autosport.
"Depending on the calibration of your sensor, it will determine your competitiveness, which is completely wrong.
"Teams will end up buying hundreds of sensors, as some manufacturers already have, to try to pick the best.
"It ends up like the tricks in go-karting, where you go through carburettors to try to find the best ones. I don't think that is an acceptable way of moving forward."
He added: "We know that some cars' fuel sensors didn't work at all in Melbourne - so we need to find a more robust and reliable way of having confidence in the FIA measurements.
"And I think that is for the teams, and the technical guys at the FIA to find a solution, because there is too much at stake to be reliant on a sensor that is drifting around or unreliable.
"F1 costs millions and millions of pounds. There needs to be a better form of measurement than what we currently have."
Meanwhile, the Brit told Sky Sports that he is confident Red Bull will be vindicated when they take their appeal before the FIA's Court of Appeal in Paris on April 14
"We're appealing on the grounds that we do not believe we've broken the rules," said Horner.
"We're extremely confident we haven't exceeded the 100 kilograms of fuel per hour that is permitted to be utilised by the car and the engine.
"That was the reason for our appeal, we feel we've a strong case, and it will be down to the appeal court to ultimately decide."
He added: "Our whole case, the whole dispute, is based on which reading is correct.
"We have a sensor (that of the FIA) that is drifting, isn't reading correctly, versus a fuel rail we know is calibrated and hasn't varied throughout the weekend.
"It has subsequently been checked, has been found to not be faulty, hasn't moved or varied at all since it was installed on to the car prior to the weekend.
"So our argument is very simple - that we haven't broken the technical regulations, haven't exceeded the fuel-flow rate, and the sensor, as we will be able to demonstrate in the appeal, is erroneous."