The incident caused the Congress of the Philippines to halt the passage of the Bangsamoro Basic Law, effectively endangering the peace process between the government and the MILF.

On Sunday, January 25, 2015, three platoons of the elite SAF police squad entered the guerrilla enclave of Tukanalipao, Mindanao, Philippines, with the goal of detaining two high-ranking Jemaah Islamiyah-affiliated, improvised-explosive-device experts, Zulkifli Abdhir (also known as Marwan) and Abdul Basit Usman.

A MILF spokesman accused the SAF squads of initiating the firefight, claiming that the rebels acted in self-defense, and proposed the continuation of the peace process.

[30] Abu Misri Mama, BIFF spokesman, said that his rebel group's relationship with the MILF's 105th Command headed by Ustadz Zacaria Guma is positive.

[13] The Philippine National Police planned ten operations, including Oplan Exodus which was implemented on January 25, 2015, targeting bomb expert Zulkifli Abdhir, also known as Marwan.

[34] The two agencies that cooperated during the battle, the Philippine National Police and the Federal Bureau of Investigation, confirmed on Wednesday February 4, 2015, at 6:30 p.m. that Zulkifli Abdhir, also known as Marwan, was officially killed during the Mamasapano encounter, based on a matching DNA test.

Then PO2 Christopher Lalan, lone survivor of the clash said, "at least 11 members of the combined forces of MILF, BIFF, and private armed groups were taken down by SAF troopers from his Company".

[43] The chairman of the Philippine Senate Committee on Local Government, Bongbong Marcos, stated that hearings regarding the involvement of security and armed forces provisions of the Bangsamoro Basic Law were halted.

Senator Alan Peter Cayetano also claimed that his coalition will withdraw its support for the Bangsamoro Basic Law, endangering the ongoing peace process.

At a press briefing at Camp Crame, PNP Deputy Director General Leonardo Espina and Secretary of the Interior and Local Government Mar Roxas announced the establishment of a board of inquiry tasked with the investigation of the police encounter in Maguindanao.

In addition, he also declared January 30 as a "National Day of Mourning", and pressed for the immediate Congressional approval of the proposed Bangsamoro Basic Law.

[46] Aquino admitted there had been a "lack of coordination" among the government forces and the MILF, that he and suspended police chief Alan Purisima personally knew of the operations, and that both Roxas and Espina were not notified of it beforehand.

[49] In an effort to mend relations with the villagers in the area where the clash occurred, in 2015 the government began construction of a bridge over the river by the field where the 44 policemen were killed.

[50] Meanwhile, when the remains of the 44 slain SAF men arrived at Villamor Air Base, President Benigno S. Aquino III was nowhere to be found as he chose to attend the inauguration of a Mitsubishi Motors Car Plant instead.

Eight months later, on September 22, 2015, criminal charges were filed by the NBI against 90 individuals, 25 from the MILF, 12 from the BIFF, and 52 from private armed group or with unknown affiliation who involved in the clash.

[52] A few months after the clash, Abdul Basit Usman, another target of the operation, was killed by MILF after being found hiding on a base command's camp.

In January 2016, retired Police Chief Superintendent Diosdado Valeroso claimed he had a recording of an exchange of words between a government official and a lawmaker as part of the evidence to be submitted in the Senate investigation on Mamasapano clash.

About 5,000 policemen, firemen, and jail guards in their uniforms trooped from the Libingan ng mga Bayani to the National Capital Regional Police Office (NCRPO) headquarters in Taguig, and called for justice for the members of the elite SAF men killed.

"Filipinos are demanding no more than the truth and genuine justice", assailing the brutality inflicted on the 44 commandos and offered a Mass specifically for the SAF 44 and their families attended by uniformed personnel led by Senior Supt.

Otherwise, it will be part of your legacy to be always hesitant, flip-flopping.” He criticized Aquino, who is also the commander-in-chief of the PNP and the AFP, for his apparent poor strategic direction and asserts that it is the soldier, the policeman, the law enforcer, the guardian of security that suffers because of his decisions.

Seven of his batchmates who killed in the clash were from the Mabalasik Class of 2008 of the National Police Training Institute (NPTI), Philippine Public Safety College (PPSC).

[67] From 2015 to 2022, Davao City mayor and later vice president Sara Duterte had her profile pictures on Facebook and Instagram set to a memorial image that reads: "Rest in peace SAF 44".

[68][69][70][71][72] Leftist militant group Bagong Alyansang Makabayan (Bayan), led by Renato Reyes Jr., questioned President Benigno Aquino III regarding allegations that he knew of the police operation citing a prior report by the Manila Standard.

At the same time, the EU envoy said the doubts raised by some quarters about the viability of the peace agreement between the government and Moro Islamic Liberation Front, including lawmakers' suspension of discussions on the proposed Bangsamoro Basic Law, was understandable.

"I think the only sensible thing I can say, when we are all trying to find out what exactly happened and why, is that how important it is for the people of the Philippines, including Mindanao, that the peace process is not discarded as a result of this tragedy and we are just hoping that that could be the case," Tweddel said.

“My thoughts, condolences to families and friends and colleagues of brave members of the Special Action Force who lost their lives this week,” Goldberg said in his Twitter account.

The embassy added that the USA reiterated its support for the Philippine government's efforts to fight international terrorism while promoting a "just and lasting peaceful resolution" to the Mindanao conflict.

[83] US Embassy Press Attache Kurt Hoyer denied allegations of any US involvement in the clash after US troops in civilian clothes were seen Monday assisting in the airlifting of the wounded.

Hoyer told MindaNews in a text message Tuesday morning (January 27, 2015) that "at the request of the Armed Forces of the Philippines, US service members serving in JSOTF-P (Joint Special Operations Task Force-Philippines) responded to assist in the evacuation of dead and wounded after the firefight in Maguindanao."

The opening sequence of London Has Fallen briefly mentions "a national day of mourning in the Philippines, after 44 police commandos were killed in the line of duty when an anti-terror operation went wrong", making it look like the antagonist of the film had links to the incident.