The row between the Philippine government and Fokker Services Asia is over who decided to send the presidential planes two engines to the United States for maintenance while the rest of the aircraft was being worked on in Singapore.
The jet, a Fokker F-28 first used by late dictator Ferdinand Marcos two decades ago, has few extravagances to set it apart from most executive aircraft other than a presidential chair topped by a presidential crown.
But Arroyo has had to trade her special seat for one on Philippine Airlines since the routine maintenance began early last year and the payment row kept her plane in Singapore.
Arroyo, who took over from Joseph Estrada in January 2001 when he was deposed, has faced criticism at home over the expense of keeping the private jet.
The hefty plane repair cost is something the government can ill afford as it battles a ballooning deficit while trying to raise the standard of living, fight corruption and fix a frayed tax net.
Some political opponents have sniped that the notion of nationalizing the Philippine Airlines fleet can hardly get off the ground if Arroyo cannot manage her own plane.
The Presidential Palace said last week it would pay for the repairs once an independent appraiser assesses the costs.
"It was Fokker who sent those engines to Dallas," Senior Deputy Executive Secretary Waldo Flores said last week, adding the work in the United States was not covered by the contract.
As the row rumbles on, Arroyos administration has paid about P75 million since January 2001 for her chartered flights around the country, he said.
No one at the Presidential Palace was available to comment on Thursday as officials focused on a bombing in the southern Philippines on Wednesday that killed a US soldier.
Michael Cole, the regional director of Fokker Services Asia, said Arroyos plane would be fit to fly once its engines and body were reunited.
"If they pay, it will all be over and the engines will come back," Cole told Reuters. "It was on the instructions of the Philippine Air Force that they were sent to Dallas."
Fokker, a Dutch company with a long history in aviation, stopped making planes after going bankrupt in 1996. Its name and four units were bought by Dutch plane maker Stork NV.
Cole said he could not comment further as the government has a case against the company pending in a Philippine court.
Flores, who met Cole in Manila last week, said then that an out-of-court settlement was possible.
The idea of selling the presidential plane came up during Joseph Estradas term in office.
But a source at the Philippine Air Force told Reuters on Thursday it was cheaper to maintain the existing aircraft than lease one outside the country and that a dedicated plane raised the level of security around Arroyo.