The unique host-guest structure of the type-II silicon (Si) clathrate offers tunable electronic structures by doping guest atoms or molecules to the Si28 cages. Here we investigate the possibility of inducing intermediate bands (IBs) by Cu and Ag atoms employing first-principles calculations based on the density functional theory. Our analyses reveal that one or two isolated Cu/Ag atoms around the cage center are required to obtain IBs useful for photovoltaics; however, further clustering is likely to occur, which removes IBs and converts these Si clathrates into metal. Specifically, the formation of Cu and Ag clusters is mainly determined by local thermodynamics and local kinetics, respectively. All the Cu-clathrate structures presenting IBs are not energetically favorable, making Cu inappropriate for IB solar cells, whereas clathrates with one or two Ag atoms inside the cage that have IBs are thermodynamically stable, but the subsequent aggregation to form 3Ag-or 4Ag-cluster will destroy IBs. Thus preventing clustering is crucial to realize IBs in Si clathates by doping noble metal atoms.