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President Susilo Bambang Yudhoyono on Friday demanded that leaders of both the Indonesian Armed Forces and the National Police to clear their ranks of misconduct.

Speaking during the two institutions’ annual joint leadership meeting in Jakarta that was attended by more than 500 high-ranking officers, the head of state raised alarming concerns.

“End markup practices in both weaponry and non-weaponry procurement,” Yudhoyono ordered.

“If there is a case that I cannot tolerate, I will ask the BPKP, BPK and KPK to take action,” he said, referring to State Finance and Development Comptroller, the Supreme Audit Agency and the Corruption Eradication Commission, respectively.

The president pointed out the government has increased the budget for both institutions, and expected them to use the funds “optimally and right on target.”

Subsequently, the president addressed the military’s human rights issues.

“I am concerned about a violation of law and discipline in Papua. Although small-scale … I want it to be dealt with,” he said. The president was referring to the torture of two Papuans by soldiers last year.

“It may seem small, an act involving just one Second Sergeant and two First Privates, but the impact is international, reaching the United Nations, Europe and the United States.”

Yudhoyono said the abuse was not a policy endorsed by the Armed Forces (TNI) or the government, but an act perpetrated by individual soldiers. The troops in the Papua case face up to one year in prison.

Yudhoyono, however, said Indonesia had made significant progress in addressing human rights concerns.

“Since 2004, there have not been any gross violations of human rights,” he said. “This is historic — a new chapter.”

The president said the Papua case was “just one incident amid a wave of change in our country over the past few years.”

Regardless, he raised the need for the TNI to continuously educate and train its members to uphold human rights principles.

The president then moved on to raise the need to maintain the utmost level of discipline and integrity in the military and the National Police.

“There are still officers who abuse their power, who do not maintain their integrity and discipline,” he said, adding that the state institutions should not protect members involved in any wrongdoings.

While the message was directed at both institutions, the president specifically pointed to the members of the National Police implicated in the Gayus Tambunan saga.

“Punish them,” he said, “so that the police can maintain the public’s trust.”

The president also urged the National Police to maintain its antiterrorism effort, including its deradicalization programs, while telling the military to be ready to assist police.

He also instructed both security forces to always be ready to be deployed for natural disaster management in times of crisis, while reminding the military that the government wanted part of its strength to be available for international peacekeeping missions.

Lastly, the president expressed the government’s commitment to improve the welfare of TNI members and police officers, including through pay raises, but called upon both “to improve your performance and achievements.”

Yudhoyono’s instructions came a day after the TNI announced its 16 priorities for this year.

At a press conference after Friday’s meeting, TNI Chief Adm. Agus Suhartono said dealing with threats against the nation’s sovereignty was topping the list.

“It’s also a priority for us to tackle any armed separatism ... especially in Papua,” he said.

Similar to last year’s priorities, Papua, Maluku and Aceh will also get a lot of military attention this year.

“The intelligence units tell us that these areas are still the most vulnerable to conflict and separatism,” Agus said.

Also on the agenda for the TNI in 2011 is dealing with the threat of religious radicalism, troop readiness for peacekeeping missions, human rights education for subordinates by unit commanders and anticipation and tackling of social unrest.