Thousands of people displaced by the conflict on the southern Philippine island of Mindanao face a growing risk of extrajudicial execution or abduction, a report by a human rights group has claimed.

According to Amnesty International, dozens of people have been killed or have disappeared, apparently targeted by members of the military who suspect them of having links with Muslim fighters.

Many others have also been the victims of attacks by the rebels themselves, the group said.

In a report on the impact of the Mindanao conflict, Amnesty warned of a "human rights crisis" on the island with more than 700,000 people driven from their homes by fighting between security forces and the rebel Moro Islamic Liberation Front (MILF).

Many of those displaced civilians "faced the risk of unlawful killings, enforced disappearances, torture, arbitrary arrests, displacement and burning and destruction of their homes," the watchdog said.

"There has been an alarming level (of these incidents) since fresh conflict began in August last year," Parong told reporters.

Many of the abuses had gone under-reported in the Philippine media, she added.

Parong said Amnesty was particularly concerned over reports that the military has labelled the displaced communities as potential MILF bases, where rebels could stage attacks on military targets.

"That is an alarming situation that would make the IDPs (internally displaced persons) targets of security forces," she said.

"In a 40-year-old conflict, the cumulative numbers of victims of human rights violations is really increasing, and it has reached very, very alarming levels."

The 12,000-strong MILF has been waging a rebellion for an independent Islamic state on Mindanao since 1978.