Cyprus said on Tuesday it had refused permission to Qatari air force jets to land at Larnaca airport and only changed tack when they reported they were running out of fuel.
"Cyprus Republic authorities did not give permission (to land), subsequently they asked for permission for an emergency landing due to lack of fuel," said Cyprus government spokesman Stefanos Stefanou in a written statement.
"Civil Aviation acting under international rules had to give permission for landing and refuelling."
He said that three aircraft landed at Larnaca, the main civil airport in Cyprus, two Mirage jet fighters and a C-17 transport plane.
"As soon as they refuel they will depart," ended the brief statement.
State television said the two French-built Mirage 2000-5 combat aircraft and the US-made cargo plane were en route to a US base in Souda, Crete.
Stefanou told the broadcaster that there was no prior warning from the Qatari government about the aircraft wanting to make an unscheduled stop in Cyprus.
Qatar was the only Arab state to agree to participate in military operations in Libya, although the Arab League has backed the UN-mandated no-fly zone to stop strongman Moamer Kadhafi's forces harming civilians in a conflict with an insurgency.
Qatari Prime Minister Sheikh Hamad bin Jassem al-Thani on Sunday said the aim was to "stop the bloodbath" and it was necessary for Arab states to take part.
A French defence ministry spokesman said Qatar had decided to deploy four aircraft in the zone.
Cyprus on the other hand has refused to be party to any military action against Libya.