Officials in Pakistan's tribal belt said the attack was carried out on the Afghan side of the border. Some media reports, however, said the strike happened inside Pakistan's Khyber tribal region.
The boat was reportedly carrying suspected terrorists from Afghanistan into Pakistan. Reports said the dead were Afghan Taliban members. Two others were injured in the missile strike by the CIA-operated drone.
In the past, drones have targeted compounds and vehicles in Pakistan's lawless tribal belt. This was the first time a boat was targeted, official sources said.
The warning was reportedly conveyed by visiting US Defence Secretary Chuck Hagel during his meetings here with Pakistani leaders. Hagel met Prime Minister Nawaz Sharif and army chief Gen Raheel Sharif during his trip.
NATO supply routes in the country's northwest have been blocked by workers of Imran Khan's Pakistan Tehrik-e-Insaf party to protest against US drone strikes.
The strikes are an emotional issue in Pakistan, which says the attacks violate its sovereignty and are counter-productive for the war on terror.
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