Federal Research Investment Act - Calls for Federal funding levels for fundamental, scientific, and pre-competitive engineering research to be increased to equal approximately 2.6 percent of the total annual Federal budget. Authorizes appropriations for civilian research and development (R&D) within specified agencies for FY 1999 through 2010.

Directs the President to include with the annual budget request a report concerning Federal R&D program funding, future R&D strategies and targets, and an analysis of funding levels across Federal agencies by funding methodology.

Requires the Director of the Office of Science Technology Policy (OSTP) to enter in an agreement with the National Academy of Sciences to conduct a comprehensive study to develop methods for evaluating federally-funded R&D programs. Requires the Director of the Office of Management and Budget (OMB), based on study results, to promulgate one or more alternative forms for Federal R&D performance goals. Permits an agency head to apply such an alternative form without further authorization by OMB. Requires agency heads carrying out R&D activities, upon updating a strategic plan, to describe the current and future use of methods for determining an acceptable level of R&D success as recommended by the study. Authorizes appropriations for the study.

Requires: (1) the OMB Director, based upon program performance reports, to identify the civilian R&D program activities or components which do not meet an acceptable level of success; (2) an agency head to submit to the appropriate congressional committees a concise statement of the steps needed to terminate a program activity or component identified as being below the acceptable level of success for two consecutive fiscal years; (3) such a program to be terminated unless the Directors of OSTP and OMB and the agency head determine that it should be continued; and (4) the statement of termination to recommend disposition of unexpended and unobligated funds from terminated programs.