Jakarta: Indonesian police detained a top anti-graft investigator on Friday to question him over his role in the deadly shooting of a thief more than a decade ago, the latest blow to the widely popular law enforcement agency.


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The Corruption Eradication Agency (KPK), popular among ordinary Indonesians for being a thorn in the side of the Indonesian establishment, has been severely weakened over the past four months in a tit-for-tat feud with the police.


President Joko Widodo has done little to protect the agency, raising questions over his anti-graft credentials in a country that Transparency International`s corruption perception index ranks below China and Niger.


KPK investigator Novel Baswedan, a cousin of Education Minister Anis Baswedan, was arrested at his home in North Jakarta after the police deemed him uncooperative with the investigation of his case.


"We have called him two times for questioning but he did not show up without proper reason," said police spokesman Agus Rianto.


Somewhat unusually, Widodo urged police not to arrest KPK investigator Baswedan.


"I command the police chief to stop making controversial moves that are not in synergy with the KPK. The KPK and the police have to work together to eradicate corruption," Widodo said in a televised statement.


Novel Baswedan is being questioned over the shooting death of a thief in 2004 while he was still serving as an investigator for the Bengkulu police on the island of Sumatra.


Indonesian media have dubbed him a "supercop" for his involvement in many successful corruption cases. Those include the 2013 graft case of Djoko Susilo, a two-star police general.


The arrest came a week after the swearing-in of Budi Gunawan as Indonesia`s No.2 police officer. Gunawan was dropped by Widodo for the top job because of a bribery scandal being investigated by the anti-graft agency.


Gunawan was previously named a suspect by the KPK, igniting the latest dispute between the two law enforcement agencies. Gunawan has maintained his innocence and managed to clear his name in a Jakarta court.


Separate police investigations have led to the suspension of two KPK commissioners, while moves by the judiciary and parliament were also threatening the agency`s future.