Retired US General Anthony Zinni set out for Aceh's sensitive Pidie district, where Indonesian troops said they shot dead two alleged separatist rebels a day earlier.
Zinni, who has mediated in talks between Indonesia's government and separatist rebels in Aceh, arrived in the province Monday as Jakarta said it was preparing for more discussions with the insurgents.
His trip to Pidie, about two hours from the capital Banda Aceh, followed a meeting Tuesday morning with Inspector General Yusuf Manggabarani, the provincial police chief.
Two officials from the Henry Dunant Centre (HDC) which has organised previous rounds of talks between the government and rebels in Geneva since 2000, accompanied the former Marine general during the closed-door session.
Zinni declined comment after the meeting, but Manggabarani told reporters that police reported the "real situation" in Aceh, where rebels from the Free Aceh Movement (GAM) have been waging a 26-year war for independence. "We asked HDC to be more neutral and transparent so a negative perception toward them doesn't occur," Manggabarani said.
The security forces in Aceh have previously questioned HDC's neutrality but Indonesia's foreign minister has said he is satisfied with its role.
Zinni then left Banda Aceh for Pidie. He was to return to the provincial capital late in the afternoon for talks with the Aceh military commander, Major General Djali Yusuf.
Yusuf's spokesman, Major Zaenal Muttaqin, said troops shot dead two men in their early twenties on Monday in Pidie's Puuk region after they allegedly opened fire. Muttaqin said troops seized a pistol, grenade and ammunition from the alleged rebels.
On Monday, Zinni held a closed-door meeting with GAM negotiators at the Banda Aceh hotel where they are based.
Amni bin Ahmad Marzuki, one of GAM's negotiators, told AFP they reported to Zinni their refusal to accept any government policy made outside of the agreement, reached in Geneva in May, for the Aceh problem to be settled through negotiations and a democratic process.
"If Jakarta makes a different policy other than what was agreed to last May, we will evaluate that as a way to shatter the dialogue process constructed since the year 2000," Marzuki said.
Jakarta's top security minister Susilo Bambang Yudhoyono had said a new Aceh policy would be announced this month. Last week President Megawati Sukarnoputri vowed tougher measures against the rebels while also offering dialogue.
Marzuki said Zinni did not make any statements during his nearly one-hour meeting with the GAM negotiators. "He was more often silent and listened to our report."
In other violence Monday, Muttaqin said a man was found shot in the head near Lhokseumawe city in North Aceh. He said the victim was a GAM member. GAM's district spokesman, Teungku Jamaika, rejected the allegation.
An estimated 10,000 people have died during 26 years of fighting in Aceh. This year alone more than 600 people, most of them civilians, have been killed.