I have Master-db server (IBM-P 2-CPU 3GHz 3 GB RAM) RHEL 5 and slave DB (IBM Intel Quad-core 3GHz 2-CPU x3650 with SAS 8GB memory) RHEL 4 64-bit.

When I run same query on Master it takes 3 minutes. Whereas on slave it takes 4 minutes, while slave is off.
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I'm not sure what your question is. Are you asking why the PPC is faster, despite having less ram and CPU power? This could be for any number of reasons. Are the machines dedicated, or are they running other processes at the same time. Is this behavior reproducible, or are these the results of just one test. If these are dedicated servers giving reproducible results, then my next question would be whether or not they have the same version of mysql installed. Given that one is RHEL 4 and the other is 5, they might not. Perhaps this just means that mysql made a large gain in efficiency between the versions in RHEL 4 and RHEL 5.