Banking regulations act of India, 1949 defines banking as “acceptance of deposits for the purpose of lending or investment from the public, repayment on demand or otherwise and withdrawable through cheques, drafts order or otherwise”, the major participants of the Indian financial system are commercial banks, the financial institution encompassing term lending institutions. Investments institutions, specialized financial institution and the state level development banks, non banking financial companies (NBFC) and other market intermediaries such has the stock brokers and money lenders are among the oldest of the certain variants of NBFC and the oldest market participants. The asset quality of banks is one of the most important indicators of their financial health. The Indian banking sector has been facing severe problems of increasing Non- Performing Assets (NPAs). The NPAs growth directly and indirectly affects the quality of assets and profitability of banks. It also shows the efficiency of banks credit risk management and the recovery effectiveness. NPA do not generate any income, whereas, the bank is required to make provisions for such as assets that why is a double edge weapon. This paper outlines the concept of quality of bank loans of different types like Housing, Agriculture and MSME loans in state Haryana of selected public and private sector banks. This study is highlighting problems associated with the role of commercial bank in financing Small and Medium Scale Enterprises (SME). The overall objective of the research was to assess the effect of the financing provisions existing for the setting up and operations of MSMEs in the country and to generate recommendations for more robust financing mechanisms for successful operation of the MSMEs, in turn understanding the impact of MSME loans on financial institutions due to NPA. There are many research conducted on the topic of Non- Performing Assets (NPA) Management, concerning particular bank, comparative study of public and private banks etc. In this paper the researcher is considering the aggregate data of selected public sector and private sector banks and attempts to compare the NPA of Housing, Agriculture and MSME loans in state Haryana of public and private sector banks. The tools used in the study are average and Anova test and variance. The findings reveal that NPA is common problem for both public and private sector banks and is associated with all types of loans either that is housing loans, agriculture loans and loans to SMES. NPAs of both public and private sector banks show the increasing trend. In 2010-11 GNPA of public and private sector were at same level it was 2% but after 2010-11 it increased in many fold and at present there is GNPA in some more than 15%. It shows the dark area of Indian banking sector.