In its latest report on the southern provinces of Narathiwat, Pattani and Yala, the human rights group found that two-thirds of the nearly 5,000 people killed in the conflict since it broke out in 2004 were civilians.
"As the insurgents have never articulated their aims, these attacks seem aimed primarily at spreading terror," said Donna Guest, Amnesty International's deputy director for Asia.
"These attacks constitute war crimes as defined by the Geneva Convention," as they target people taking no part in hostilities, she told a press conference.
According to Amnesty's report, They Took Nothing But His Life, between January 2004 and June 2011 there were 10,890 incidents of violence in the South, resulting in 4,766 deaths and 7,808 injuries.
Although a separatist struggle has simmered in the three southernmost provinces - once constituting the independent Islamic sultanate of Pattani - for more than 100 years, the conflict took a more violent turn in January 2004, when Muslim militants raided an army base, killing four soldiers and stealing 300 weapons.
Over the past seven and a half years, various Thai governments have responded by imposing harsher legislation in the region, including martial law, an emergency decree and the internal security act.
The Amnesty report noted that insurgent attacks on civilians appeared to escalate after a coup that resulted in a military-appointed government taking power in 2007.
That year, the military, which has 40,000 troops based in the three provinces, started carrying out sweeps of local villages and detained numerous suspected insurgents.
Little is known about the exact nature of the southern insurgency, which includes such groups as the National Revolutionary Front.
Nearly 90 per cent of the 2 million people in the region are Muslims, making it the only majority Muslim area in predominantly Buddhist Thailand.
The region, which borders Malaysia, is also known to be rife with crime such as smuggling, drug trafficking and extortion.
"In southern Thailand, it is no secret that the insurgency provides amazing cover for other kinds of criminal activities," Amnesty's Thailand director Benjamin Zawacki said..
"But all that exists on Thailand's other borders, and nowhere else are there two people killed a day," he said.
He acknowledged that Amnesty's call on the insurgents to stop their attacks on civilians, or risk being held liable for human rights abuses, was "a bit pie in the sky."
"It is ultimately the Thai government's responsibility to ensure the well-being of all Thai citizens," Guest said. "The government must ensure that their counter-insurgency strategy has a strong human-rights component."