The Philippines Navy said it had detained 35 suspected Filipino militants on Wednesday as they sought to sail home from a military offensive against them in the Malaysian state of Sabah.
They are believed to be remnants of a band of up to 300 followers of a self-proclaimed Filipino sultan who entered Sabah a month ago to stake a territorial claim to the area, regional military chief Rey Ardo said.
"They were coming back (home)... they are armed," Lieutenant-General Ardo said on ABS-CBN television, confirming less detailed reports of their arrest by the Philippine Navy.
The self-proclaimed Sultan of Sulu, whose ancestors ruled over parts of the what is now the southern Philippines and Sabah centuries ago, vowed his men would not leave until Malaysia recognised their territorial claims.
However after a stand-off that lasted more than two weeks, Malaysian security forces launched a major operation against the gunmen.
Malaysian authorities have reported that 64 people have been killed, mostly militants, and 97 followers of the sultan have been arrested in Sabah. Security operations are continuing.
The 35 people seized on Wednesday were on two small boats that were intercepted by two navy patrol vessels on the Philippine side of the sea border with Malaysia, navy spokesman Lieutenant-Colonel Gregory Fabic told AFP.
They were sailing to a Philippine island about 60 kilometres (35 miles) from the area of Sabah at the heart of the security offensive, according to Ardo, the regional military commander.
Fabic and Ardo said there were 34 men and one woman aboard the boats, both of which carried guns.
Ardo said one of the men was wounded, possibly from the Sabah clashes.