The OP is from 2011. So as of end of 2015 I would like mention that there is a new kid in town which claims to be numpy for java -> nd4j]. The nice thing is that nd4j is an abstraction layer on top of different libraries like blas. Depending on the size of your matrices there are underlying implementations twice as fast as numpy or jblas. And your code is real platform independent.

org.nd4j.linalg.api.ndarray.INDArray arr = org.nd4j.linalg.factory.Nd4j.create(new double[][]{
                {1, 5, 0, 6, 2, 0, 9, 0, 5, 2},
                {3, 6, 1, 0, 4, 3, 1, 4, 8, 1}
        });

        org.nd4j.linalg.indexing.INDArrayIndex indices[] = {
                org.nd4j.linalg.indexing.NDArrayIndex.all(),
                new org.nd4j.linalg.indexing.SpecifiedIndex(1,5,6)
        };

        org.nd4j.linalg.api.ndarray.INDArray selected = arr.get(indices);
        System.out.println(selected);
    }

This should work for you. This prints: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

[[    5.0000,         0,    9.0000], 
 [    6.0000,    3.0000,    1.0000]]

Process finished with exit code 0