This study uses the flow of funds accounts framework and undertakes an in-depth analysis of the inter-sectoral mobility of capital in India. Unlike previous studies, the FH model is estimated at the sectoral level using annual data for the period 1950–51 to 2012–13. The model estimated in one-regime setting with no structural break provides a weak and mixed support and that estimated in a sample-split setting with a single structural break provides no support for the presence of a long-run relationship between saving and investment for all the sectors. In contrast, the model estimated with multiple structural breaks provides dominant support for the presence of cointegration between saving and investment for all the sectors. The end-of-sample cointegration breakdown tests suggest the breakdowns of cointegration between saving and investment in all the sub-sample periods for the household and PCB sectors, but not for the public sector. The FOF accounts could be used to monitor the borrowing and lending operations of both financial and non-financial sectors and to identify any deformities in the system. The regulatory and supervisory policies need to be put in place promptly to resolve the identified deformities at their early stages, before they magnify and make the entire system dysfunctional.