Egyptian border guards discovered the fuel shipment while monitoring a tunnel smuggling area on the Egyptian side of Rafah, sources said.
In late January, Qatari-donated fuel to Gaza was suspended due to the security situation in Egypt.
Violent clashes between Sinai armed groups and Egyptian forces led to a suspension in deliveries last November, but they resumed earlier in January.
The Qatari fuel is part of 27 million liters donated by the Gulf state to ease Gaza's energy crisis.
Last week, Egyptian forces began flooding smuggling tunnels under the Gaza border in a campaign to shut them down. The tunnels have provided a lifeline to Palestinians since Israel intensified its blockade of the Gaza Strip in 2007.