I am solving a matrix iteratively and after 2 iteration it becomes ill conditioned. Few of the Eigen values are negative also.I found some methods for ill conditional matrix but they are for symmetrical and positive definite matrix.
You should solve the matrix equation using Gaussian elimination with full pivoting. ( with the matrix elements in double precision)
A matrix reduction sequence usually becomes ill conditioned when a very small number appears in the pivot element. Pivoting eliminates this problem by searching for the largest matrix entry and using it as the pivot.
I hope you know about this procedure. It is not frequently used because it requires a specially written program that can manage the exchange of columns and rows of a matrix.
Do a google search to see if you can locate such a program online. Otherwise a visit to your University library can locate the program in a handbook of programs.