The administration camp said its preliminary count showed a 12-0 sweep of the province - with not a single opposition candidate making it on the ballot.
Volunteers from an independent watchdog authorised by the elections commission to do a quick vote count complained that they were not allowed to monitor the canvassing of votes and were not provided with election returns from the province.
Benjamin Abalos, the elections commission chairman, said it was conducting an investigation because "the credibility of the commission has been put at stake".
The investigation comes two days after a newly re-elected mayor and a provincial official were killed by an attacker in northern Ilocos Norte province.
The mayor's security guard killed the attacker as he tried to flee a packed auditorium on Sunday, police said.
Philip Velasco, the mayor of Bacarra town, and other provincial board members who won seats in last week's elections were among the guests in the auditorium when the unidentified gunman shot the mayor several times.
Provincial board member Marecelino Andaya, who was seated near the mayor, also died in the attack.
Three people were wounded, including a 9-year-old boy, Chief Superintendent Leopoldo Bataoil, the regional police chief, said.
Police say 41 people have died in politically motivated killings since the start of the election campaign on January 14. They said they were still investigating if the latest killings in Ilocos Norte were election-related.