The union has been plagued by a cash crisis which has led to flight delays since August 21 across the country, but it was thought that a resolution had been reached after the government pledged to provide AirUnion companies with 24,000 tons of fuel last week.
Four passenger flights by KrasAir, one of five regional carriers within the alliance, have been delayed in the airports of Krasnoyarsk in East Siberia and Yuzhno-Sakhalinsk, in Russia's Far East.
"Three flights have been delayed in Yuzhno-Sakhalinsk since Friday," KrasAir press secretary Lyudmila Ganzhurova said. "We paid a certain sum for fuel to a supplier in Yuzhno-Sakhalinsk Friday, but the company said it had not received the money."
"Talks have been ongoing since early morning," Ganzhurova said, adding that another flight could not leave Krasnoyarsk airport for Yuzhno-Sakhalinsk due to the lack of space in the local airport.
Russian Prime Minister Vladimir Putin approved the merger of five air companies into AiRUnion in May. The move was designed to consolidate and modernize the domestic industry. Earlier reports said the state would hold no less than 45% in AiRUnion.
The alliance was seen as a rival to market leaders Aeroflot and S7. AiRUnion's total passenger turnover in 2007 was 3.6 million.
Media reports earlier said fuel prices had risen 70% in Russia since the start of 2008. The authorities have ordered a series of anti-trust probes against suppliers and producers.
AirUnion's aggregate debts currently stand at over $1 billion.
