Metro Manila (CNN Philippines, October 23) — The long-running dispute between the government and the maintenance provider of the troubled Metro Rail Transit 3 (MRT-3) now includes transport officials from the previous administration.

Transportation Undersecretary for Legal Affairs Rainier Yebra filed on Monday a graft complaint at the Ombudsman against former Transportation Secretary Jun Abaya and other former officials of the Department of Transportation and Communications (DOTC).

This is for the allegedly anomalous maintenance contract with Filipino-Korean company Busan Universal Rails, Inc. (BURI).

"This has everything to do with the current degradation, the poor service, the unreliable trains that we have at the MRT-3," Yebra said.

BURI officials are also included in the complaint.

The DOTr on Friday threatened to terminate BURI's three-year contract, which expires in January 2019, for the company's alleged poor performance, among other reasons.

Read: DOTr threatens to terminate MRT maintenance provider's contract

BURI Legal Counsel Charles Mercado told CNN Philippines' "Balitaan" on Friday that the company's job is not to prevent glitches, but to fix glitches as these occur.

"Binabaliktad lang kami ng DOTr," he said. "Sinasabi nila, kasalanan namin yung glitches. Bakit namin gugustuhin na magkaroon ng glitch, eh may mga sumasakay? Ayaw naman naming masaktan yung mga tao o magkaaberya."

[Translation: The DOTr is twisting us around. They say the glitches are our fault. But why would we want glitches to happen, but there are people riding the train? We don't want people to get hurt or be inconvenienced.]

Billions allegedly defrauded

Yebra said Abaya and the other respondents defrauded the government of billions of pesos when it let BURI, which Yebra called an unqualified service provider, handle the MRT-3's maintenance.

The complaint said the government awarded in December 2015 the maintenance contract of about ₱3.81 billion to Busan Joint Venture (JV).

But Yebra said an entirely different entity, BURI, has been implementing the contract and was formed in January 2016 allegedly on orders of Abaya and other transport officials.

"Busan Joint Venture won the contract with then-DOTC and one of joint venturers there is Busan Transportation Corporation," Yebra said. "Siya yung may experience, may required capitalization [That had the experience and the required capitalization]. Joint venture should've included Busan Transportation Corp."

"Instead, they formed BURI, where Busan Transportation Corporation, the Korean giant, only got 4.7-percent equity and we believe that in itself is anomalous," he added.

The complaint said aside from not being part of the bidding, BURI did not have the required 15 years of experience to be accepted as a maintenance provider.

It added that the government suffered "undue injury" because of the over ₱921 million paid to BURI so far for the "payment of dismal services."

Abaya said in a Monday statement that although he has yet to read the complaint, he looks forward to clearing his name.

"In any event, our decision has always been guided by our conscience and our compliance with procurement laws and laws with regard to the procurement of the maintenance provider," he said.

Meanwhile, BURI said on Monday that it "is confident that it will be able to answer and negate any charges against the company or its officials."

Other alleged anomalies

Abaya also faces four more graft cases at the Ombudsman for his involvement in the ₱1.72 billion Contactless Automated Fare Collection System project, the purchase of ₱3.8 billion worth of license plates and ₱3.8 billion worth of train coaches from China.

A full-blown investigation by the Senate Public Services Committee found that out of the 48 train coaches delivered, only 29 had a signaling system installed.

Read: Senate to back filing of charges vs. former transport officials over defective MRT trains

The committee also found that each of the trains weighed just over 49,000 kgs, some 3,000 kgs over the 46,300-kg limit under the terms of the contract.

Senator Grace Poe, chairman of the Senate Public Services Committee, said ₱526 million of taxpayers' money was wasted in the purchase of light rail vehicles for the MRT-3.