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The US is also sharing commercial satellite imagery with the Nigerian government, officials said.
It comes after militants released a video of about 130 girls, saying they could be swapped for jailed fighters.
Boko Haram seized them from a school in the northern Borno state on 14 April, according to BBC.
"We have shared commercial satellite imagery with the Nigerians and are flying manned ISR (intelligence, surveillance and reconnaissance) assets over Nigeria with the government's permission," a senior administration official, who declined to be named, said.
A team of about 30 US experts - members of the FBI and defence and state departments - is in Nigeria to help with the search.
The BBC's Rajini Vaidyanathan in Washington says the types of aircraft deployed haven't been revealed, but the US does have sophisticated planes that can listen into a wide range of mobile phone and telecommunications traffic.