(CNN Philippines) —  It's been over a year since the pork scandal was exposed.

Janet Napoles, along with some of her employees, and three senators who were linked to the scandal are now behind bars.

But how about others who were involved in a similar deal?

A special government audit report in 2013 names 82 questionable nongovernment organizations. Not all were operated by Napoles.

CNN Philippines found documents that show that some of them made deals questioned by the Commission on Audit under the watch of President Benigno Aquino III.

The COA report says Kabuhayan Kalusugan Alay sa Masa Foundation, Inc. (KKAMFI) goit P526.679 million from the Priority Development Assisstance Fund (PDAF) from 2007 to 2009.

A check with the Securities and Exchange Commisison (SEC) revealed the NGO's 2012 statement of sources and application of funds. It shows that it had projects with funds coming from the pork barrel of three lawmakers - Reps. Francisco Matugas, Mariano Piamonte Jr., and Baby Aline Vargas Alfonso. The funds totaled P5,990,420.

Another COA report shows that another questionable NGO — the Gabay at Pag-asa ng Masa Foundation, Inc. (GPMFI) — also had projects with 10 lawmakers from 2012 to 2013. The total pork barrel funds involved amounted to P73,836,500.

The lawmakers involved in the projects were Reps. Rodante Marcoleta, Marinao Piamonte, Abigail Faye Ferriol, Leopoldo Bataoil, Baby Aline Vargas Alfonso, Eduardo Gullas, Julieta Cortuna, Francisco Matugas, Sherwin Tugna, and Loreto Leo Ocampos.

Little progress in probe

Justice Undersecretary Jose Justiniano admits that the has been little progress in efforts to go after questionable NGOs not linked to Napoles.

Justiniano, who's assisting the Office of the Ombudsman in its probe of the pork barrel scam, says: "If you can call it progress, that's minimal."

Dr. Antonio Contreras, a political science professor at the De La Salle University in Manila, isn't convinced of the Aquino administration's sincerity in going after those who earned from kickbacks.

"It's no longer for truth or for justice's sake," he says of the efforts to go after those behind the scam.

It appears to him that these efforts are being used "as instruments to punish, to inflict misery on political enemies and then to protect and favor political allies."

Of the 10 lawmakers who allegedly dealt with KKAMFI and GPMFI in 2012 and 2013, three are administration allies:

Surigao del Norte Rep. Francisco Matugas, a leader of the president's Liberal Party, who's also facing a plunder complaint before the Office of the Ombudsman

CIBAC partylist Rep. Sherwin Tugna, who served as prosecutor in the impeachment trial of Supreme Court Justice Renato Corona

Former Misamis Occidental Rep. Leo Ocampos, who is among the top LP officials in Mindanao

As of this writing, only Tugna has responded to CNN Philippines' efforts to get their side.

He denied dealing with GPMFI, saying that the project, which cost P2 million, was coursed to the Department of Agriculture: "We put the fund in the DA and carried out the project with the DA.. Our office did not carry out a livelihood project with the Gabay ng Pag-asang Masa Foundation, Inc., a nongovernment organization. Neither did we use our Priority Development Assistance Fund for any GPMFI project."

No protection from Palace

Malacañan denies protecting its allies.

"Siyempre ang nais natin ay mas marami pa sanang konkretong resulta. Pero sa kabilang banda naman, isinasaalang-alang din natin yung proseso ng ating batas, kung saan nagbibigay naman tayo ng due process," Presidential Communications Secretary Herminio Coloma Jr. says.

[Translation: "Of course, we would like to see more concrete results. But, on the other hand, we have to take into consideration legal processes. We have to give them due process."]

Considering that the president is dealing with a number of problems and that 2016 is fast approaching, Contreras says the chief executive would not risk losing allies.

In August5 2013, the president tapped the Inter-Agency Anti-Graft Coordinating Council probe and file charges against all those involved in the pork barrel scam.

The council has yet to give an update on its efforts to go after NGOs not linked to Napoles.

"If I am invited to attend any meeting pertaining to the non-Napoles NGOs... I will attend," he says.

But so far, he has not received invitation.

Justiniano says investigators are having a hard time moving cases involving NGOs because they don't have a whistle blower.

"The only thing that COA report would establish would be dim issues of the PDAF," he said. "But even then, the report is hearsay."

But Contreras says this is nothing but an excuse because investigators already have a paper trail to work with.

Watch Part 2: Pork scams beyond Napoles

Watch Part 3: Pork scams beyond Napoles