Johnson-O'Malley Supplemental Indian Education Program Modernization Act This bill requires the Department of the Interior to annually update the number of Indian students eligible for the Johnson-O'Malley Program (JOM Program). The JOM Program awards contracts to tribal organizations, schools, states, and others to educate Indian students. Under the program, the contract amounts are based on the number of students served. Under the bill, contracting parties must annually report to Interior on the number of students they serve and how the amounts for which contract funds were used. If they fail to submit the report, Interior shall not give them program funds for the fiscal year following the academic year for which the report should have been submitted. This bill allows Interior to make recommendations for legislation to increase funds per eligible student and to identify additional sources of funding that do not reallocate existing funds utilized by Indian students. The bill allocates appropriations for any fiscal year for which the appropriated amount exceeds the previous fiscal year appropriation. Interior must confer with Indian tribes, state and local education agencies, and Alaska Native organizations that have not participated in the program to determine their interest in the JOM Program. This bill requires the Government Accountability Office to review the implementation of this bill.