The P3 billion is partial compensation for the governments seizure of the terminal from Philippine International Air Terminals Co. (Piatco) in 2004.
The Pasay City regional trial court is still determining how much the final amount should be.
Cabinet officials, meanwhile, said the government would immediately comply with the Pasay courts ruling to compensate Piatco for NAIA-3, but insists that Piatco share the initial and succeeding payments with its foreign partners.
Justice Secretary Raul Gonzalez and Trade Secretary Peter Favila in separate interviews said the decision would no longer be appealed and that it would take weeks before the P3 billion held in escrow would be given to Piatco owing to some banking procedures.
Favila and Gonzalez are members of the Cabinet Policy Group, headed by Executive Secretary Eduardo Ermita, handling the NAIA-3 case that met late yesterday afternoon at Malacañang. Other members of the policy group are Solicitor General Antonio Eduardo Nachura and Transportation Secretary Leandro Mendoza.
"We will immediately comply," Gonzalez told reporters after the meeting. "What is important is the government is acting in good faith."
On March 27, the court ordered a partial compensation payment made but the government filed a motion questioning it.
The Office of the Solicitor General, which represented the government, had earlier argued that the terminals actual value must first be determined and the facility thoroughly inspected before any payment can be made, citing a recent collapse of a section of a ceiling at the still idle terminal.
It maintained that any payment would be unfair until it was certain of the buildings structural integrity, arguing it was necessary to ensure public safety.
Judge Jesus Mupas said the ceiling collapse was irrelevant to the dispute.
"It did not create a substantial change in the rights or relations of the parties which would render execution of a final judgment unjust, impossible or inequitable, making it imperative to stay immediate execution in the interest of justice," Mupas said in his ruling.
He stressed that the P3 billion "merely represents the proffered value of the NAIA-3 facilities, that is, it merely forms part of the total amount of the just compensation to be paid to Piatco, which is still to be determined by this court."
"Hence, the plaintiffs, by nonpayment of the proffered value, do not have the right to possess NAIA Terminal 3 and should relinquish possession thereof to Piatco," Mupas ruled.
Mupas payment order stemmed from an earlier ruling made last year by Judge Henrick Gingoyon, who first handled the dispute.
The case went to Mupas when Gingoyon was murdered by three men on New Years Eve. The killing was not connected to the court battle over the terminal.
Gingoyon had ordered the government to pay an initial P3 billion as partial compensation. The government questioned his order before the Supreme Court, which ruled in favor of Piatco, however.
The tribunal said "it would be unfair for the government to take over the operation of the NAIA Terminal 3 without paying Piatco a single centavo."
It tasked the Pasay court to determine the total "just compensation" that Piatco should receive.
Gonzalez and Favila said the turnover of P3 billion to Piatco should immediately be followed by the writ of possession from the court, which formalizes the governments possession of NAIA-3 after it took over the airport in December 2004.
"Documents must change hands," the justice chief said.
The government seized the terminal from Piatco in December 2004 after the Supreme Court upheld the governments decision to unilaterally cancel its contract with Piatco for the construction of the terminal due to anomalies in the contract. With Paolo Romero, Sandy Araneta