Foreign Affairs Secretary, Albert del Rosario, called for the more than 200 armed followers of Filipino Sultan Jamalul Kiram III to surrender, saying they will not be charged upon their return to the Philippines.
Secretary del Rosario met Malaysia's foreign and defence ministers, saying afterwards relations between the two countries remain strong despite the Sabah stand-off.
He said negotiations for a peaceful end to the territorial crisis which so far has killed at least 27 people are continuing.
The gunmen, who landed on the shores of Sabah on February 12, have been claiming ownership of Sabah island by historical right.
In Manila on Wednesday, more than a hundred people staged a rally for the second straight day, calling for a peaceful end to the crisis.
Meanwhile, hundreds of Filipinos living in Sabah have travelled to the southern Philippines to escape the violence.
'Long time coming'
CEO of Kuala Lumpur's Kini-TV, Yong Kai Ping, told Radio Australia's Asia Pacific the conflict was 'a long time coming', and linked to identity cards on the island.
Mr Yong said in past years many Filipino Muslims who came to Sabah as illegal immigrants had been offered identity cards in exchange for their votes.
"There are many questions surrounding the growth of population in Sabah, that it's extremely high," he said.
"There was some calculation that growth for the last few decades, the growth was around 300 per cent."
Mr Yong said Malaysian authorities were being "tight-lipped" about "a lot of information" to do with the conflict.
"I think the authorities have not been able to release or give the public a clearer picture," he said.
"I think the general feeling is one of fear and a lot of the unconfirmed rumours going around."
Mr Yong said people were stocking up on food and water in the fear that the conflict would spread to other areas.