A Philippine military court has dismissed charges against two elite officers whose orders allegedly led to the deaths of 19 soldiers at the hands of Muslim rebels, a court official said Wednesday.

This leaves only two other officers still facing courts-martial over last year's incident, in which soldiers hunting al-Qaeda-linked militants clashed with fighters of the larger Moro Islamic Liberation Front (MILF).

Four officers, all special forces commanders, were charged with negligence over the botched operation which resulted in the deaths of the soldiers on the strife-torn southern island of Basilan.

The charges against Colonel Alexander Macario and Lieutenant Colonel Orlando Edralin were dismissed for "insufficient evidence", said Colonel Jose Feliciano Loy, a member of the court martial.

The two can now return to full-duty status, he added.

However charges remain against two other officers including Lieutenant Colonel Leonard Pena who commanded the ill-fated unit, he added.

He did not elaborate on why charges were dismissed against some officers while retained for others.

The soldiers' clash with the MILF sparked one of the biggest battles with the rebel group since it signed a ceasefire with the government in 2003.

It ignited new fighting that jeopardised the shaky peace process between the government and the MILF, which sought a separate Muslim state in the south of the Philippines.

The MILF had admitted killing the soldiers, saying five of their own fighters also died, but insisted they were only defending themselves.

Peace negotiations continued despite the renewed fighting. Last month, both sides signed a historic peace pact to end the conflict by 2016 and pave the way for a Muslim autonomous area in the south.

The Muslim rebellion in the south killed about 150,000 people, with most of the deaths coming in the 1970s when all-out war raged.