Muslim official Sama-aeh Srirako, 58, was shot in the head early on Friday in Narathiwat province while on his way to a mosque, police said.
Usman Doloh, 40, a Muslim teacher, was also shot and killed on Friday while returning home in Yala province, a police spokesman told reporters.
Friday's deaths came as a Thai army commander who ordered an assault on a mosque which killed 32 Muslim activists in the
country's south in April confirmed he would face a tribunal
investigating the attack.
General Panlop Pinmanee told AFP he would appear in a Pattani provincial court on 14 October as part of an investigation ordered by the government into whether the army overreacted when it stormed the building.
"I will testify as a witness but not as a suspect, which is in line with judicial procedure whenever there are extra judicial killings involved," Panlop told AFP.
An army spokesman said Pattani military force commander Colonel Mana Khongpaen and Lieutenant Colonel Thanapat Nakchaiya, who led the 40 soldiers involved in the mosque siege, would also testify on the same day.
The government and army have come under repeated criticism from human rights groups over their handling of the mosque siege.
The army is under fire from
human rights groups
A fact-finding commission has already concluded that troops were too heavy-handed when they stormed the Krue Se mosque during a day-long rebellion in which 108 Muslims and five security men were killed in southern Thailand.
Soldiers used grenades and heavy weaponry against the lightly armed Muslim separatists who fled to the mosque after attacking a checkpoint, according to a summary of their report released in August.
A Muslim separatist insurgency flared sporadically for decades
in the south of the overwhelmingly Buddhist kingdom until the late 1980s when the movement fragmented.
It reignited in January when insurgents stormed a southern army depot and killed four soldiers.
Thai Prime Minister Thaksin Shinawatra returned to Bangkok
on Saturday morning after a one day tour of Pattani province - one of the worst hit by the violence - with Queen Sirikit.