In current Bose-Einstein condensate experiments, the shot-to-shot variation of atom number fluctuates up to 10%. In here, we present a procedure to suppress such fluctuations by using a nonlinear p-pi-pbar matter wave interferometer for a Bose-Einstein condensate with two internal states and a high beam-splitter asymmetry (p, pbar not-equal 0.5). We analyze the situation for an inhomogeneous trap within the Gross-Pitaevskii mean-field theory, as well as a quantum mechanical Josephson model, which addresses complementary aspects of the problem and agrees well otherwise.