The South African Air Force later reported that a mayday signal had been picked up from an emergency beacon.
A spokesman for the search unit said the signal was picked up by a French aircraft helping in the search for the missing planes.
"The information is that a mayday call signal has been received by a French C160 in the area we're looking in." a spokesman said.
Later he said that an indistinct voice had been heard in the distress call. "It's sometimes a beacon signal that goes off but it can also be a voice. It was not very clear but, yes, it was a voice that came across."
A spokesman for the German defence ministry said: "It cannot be ruled out that the missing [German] plane possibly collided with an American military aircraft and crashed,"
The Pentagon later confirmed that a US Air Force C-141 Starlifter cargo plane was missing in the same region as the German plane. "They both went missing at about the same time and about the same area," a spokesman said.
The South African air rescue service also said it believed there had been a collision between the two planes. A spokeswoman said a flash was picked up overnight which could indicate the whereabouts of the missing aircraft.
The German aircraft, an eight-year-old Tupolev 154 inherited from the East German army, disappeared about 1,000 miles west of Angola on Saturday. It was carrying 12 marines, 10 crew members and two of their wives who had been invited to Cape Town for a regatta celebrating the 75th anniversary of the South African navy.
The US plane was flying from Windhoek in Namibia to Ascension Island. It was due to land at 5.51 GMT on Saturday but never arrived.
A German Airbus with a search team on board was due to fly out to the region yesterday evening and would head either for Cape Town or Pretoria depending on any new information received during the journey.
A second German airforce aircraft was due to follow the route of the crashed plane to South Africa from Dakar in Senegal via Windhoek in Namibia in search of clues.