Abu Sayyaf gunmen opened fire on the vehicles in Talipao town before dawn in what appeared to be an ambush related to a clan feud, said local marine commander Brigadier-General Martin Pinto.
"There were civilians as well as children among the 16 dead," he told reporters, without giving more details immediately about those who died.
A number of policemen were riding aboard the two vehicles, he added, although he did not say if they were among the dead.
The Abu Sayyaf was founded in the 1990s with seed money from Osama bin Laden's al Qaeda network, and is blamed for the worst terrorist attacks in the Philippines' recent history.
These include the 2004 bombing of a ferry that left more than 100 dead, abductions of foreign missionaries and tourists, and beheadings mostly of local people.
The Abu Sayyaf is believed to be holding several hostages, including foreigners, in the jungles of Jolo, one of its remote strongholds in the south of the Philippines with mostly Muslim populations.
Pinto said the attack in Talipao appeared to be an offshoot of a local feud between two Muslim clans, one of them related to Abu Sayyaf members.
The blood feuds, usually involving land disputes or previous unresolved murders, at times last decades.
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@Gaza: Is only life from Muslim majority regions important to you?
We should help the Filipinos in combating these terrorists. R.I.P.
So what ? Gaza is burning .