Speaking in a video obtained by French news agency Agence France Presse, the militants' leader said the girls will not be released until Boko Haram prisoners were freed.
He then showed what he said were about 130 of the girls, wearing full-length hijabs and praying in an undisclosed rural location.
The latest claims comes shortly after governor of Nigeria's Borno state announced he had information about the whereabouts of the girls.
Governor Kashim Shettima said he had passed reports of the sightings of the girls to the military for verification.
He then added that he did not think the girls had been taken across the border to Chad or Cameroun, contrary to what Shekau had said.
Boko Haram, which opposes the westernisation of Nigeria and tries to impose sharia law in the country, kidnapped almost 300 girls on 14 April.
About 50 of them later managed to escape, but some 220 are still estimated to be missing.
Shortly after the abduction, Shekau released a video in which he said the girls would be sold in the market place as willed by Allah.
The mass abduction has sparked international outcry.
Several NGOs have urged the militants to release the girls and put an end to their reign of terror in Nigeria.
The US announced it will send intelligence and hostage negotiation experts to help find the missing girls.
Later, the UK, France and China also offered help.
Israel said it would send an-anti terrorism team to join the search.
The militants are suspected of having laid land mines and booby traps to prevent the schoolgirls from being rescued.