It is possible to visit the pristine jungle found in the Reserve Zone of the Manu Biosphere Reserve even if you are short on time.  Here are some tour companies with shorter trips that go into the Reserve Zone which is on the Manu River, past the Limonal Ranger Station, and does require a permit to enter.  Flights were between Cusco and Boca Manu.  These prices were current as of February 2007.

Some of these do not include the $50 entrance permit fee but Mayuc and SAS do include it. Accomodations differ but all are within the Reserve Zone.