Masses of the eta and eta-prime mesons are estimated in Nf=2+1 lattice QCD with the non-perturbatively O(a) improved Wilson quark action and the Iwasaki RG-improved gluon action, using CP-PACS/JLQCD configurations on a 16^3 x 32 lattice at beta=1.83 (lattice spacing is 0.122 fm). We apply a stochastic noise estimator technique combined with smearing method to evaluate correlators among flavor SU(2) singlet pseudoscalar operators and strange pseudoscalar operators for 10 combinations of up/down and strange quark masses. The correlator matrix is then diagonalized to identify signals for mass eigenstates. Masses of the ground state and the first excited state extrapolated to the physical point are m_eta= 0.545(16) GeV and m_eta-prime= 0.871(46) GeV, being close to the experimental values of the eta and eta-prime masses.
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