The Philippines has begun its investigation into the fateful shooting of one Taiwanese fisherman by a Philippine patrol boat last week.

Evidence are now being gathered by the National Bureau of Investigation including weapons found inside the Coast Guard vessel involved in the firing incident.

NBI Chief Nonnatus Rojas particularly assured Taiwan of a thorough and objective investigation. "Our actions will be based on evidence solely, so whatever the evidence will show us, if we have to charge some people, we will charge criminal offence, we will do that," he said.

One of the evidence being closely examined is a video recording taken by some witnesses that was sent to the NBI.

Investigators are hoping that the video will be helpful in shedding light as to what really transpired, but adds that this has to be carefully verified first.

"What we are trying to establish first is the authenticity of the video. We are now interviewing and getting information from the guys who might have taken this video, before we can say that this video has relevance to this case," NBI Deputy Director Virgilio Mendez said.

The fisherman, Hung Shih Cheng, was shot dead last week in disputed waters south east of Taiwan and north of the Philippines.

The Philippine Coast Guard has already owned up to the shooting but emphasised that it only did so to defend themselves as the Taiwanese fishing vessel tried ramming their boat.

Taiwan earlier declined the apology of the Philippines saying it lacked sincerity and authority, and imposed sanctions including the suspension of work applications by Filipino overseas workers and the recall of its envoy in Manila.

"As per the the Council of Labour of the ROC (Republic of China) mandate, effective May 15, 2013, all work permit applications of Filipino blue-collar workers, including first time applications, substitute, and re-hiring are frozen," Taiwan Economic and Cultural Office Public Affairs Director Cheng Pang said in a the statement to the media.

On Thursday, after expressing continued dissatisfaction on the way Manila is handling the case, Taiwan imposed additional sanctions which included a travel advisory against the Philippines and the conduct of military drills in South China Sea.

Taiwan also sent its own investigating team on May 16 to work with local investigators for a joint inquiry.

But the Philippines' Department of Justice turned down the move as the Taiwanese investigators reportedly neither informed them of their arrival nor issued a formal request for a joint investigation.