Group Captain Peter Hackett completed a short flight in an Ikarus C42 microlight aircraft at an airfield in Gloucestershire, western England, earlier this month.
"Zero Petroleum's synthetic UL91 fuel is manufactured by extracting hydrogen from water and carbon from atmospheric carbon dioxide," the MoD said in a statement on Wednesday.
"Using energy generated from renewable sources like wind or solar, these are combined to create the synthetic fuel."
The ministry said it had the potential to save 80-90 percent of carbon per flight and help the air force's aim of using synthetic fuel to power fast jets in the future.
"This is a world first 'innovation'," said minister for defence procurement Jeremy Quin, whose government has set a target of Britain reaching net zero carbon emissions by 2050.
"Whilst green technologies like electric and hydrogen power generation are viable for many RAF platforms, high-performance aircraft require a liquid fuel alternative, like the UL91, to maintain operational capabilities."
The aviation industry -- one of the biggest emitters of greenhouse gases -- has embarked on a major effort to green its image and to develop less polluting fuels.
The RAF -- motto "per ardua ad astra" (through struggle to the stars) -- is planning its first airbase to be net zero by 2025 and be carbon neutral across the service by 2040.
Synthetic or electrofuels (e-fuels) use hydrogen, produced by electrolysis, and capture carbon dioxide from the atmosphere.
By recombining the two, fuel similar to aviation kerosene is obtained.
To be environmentally friendly, the electricity needed to produce it must be decarbonised, and come from renewable or nuclear sources.
These cutting-edge technologies are experimental but are still much more expensive than renewable fuels that are being widely tested by the industry, and cost more than kerosene.
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