During the initial stage of AI's incorporation into scientific research, AI systems have functioned predominantly as tools under direct human supervision and control. However, AI incorporation into scientific research is now entering a stage in which AI Agents perform research tasks with partial autonomy while remaining under human supervision and control. In the not-too-distant future, a third stage may arise when autonomous AI systems conduct their own research and generate knowledge without human supervision or control. While the second and third stages of AI-augmented research may offer substantial benefits for science and society, they also create novel ethical issues, including (1) Conducting immoral research that may harm humans and other forms of life; (2) Increasing rate of biased, erroneous and deceptive research; (3) Confidentiality challenges; (4) Overreliance on AI; (5) Diffusion of responsibility and accountability; (6) Deskilling; (7) Job losses; (8) AI-generated research beyond human comprehension; and (9) Erosion of trust. We suggest specific solutions to minimize the negative consequences of these issues and offer proposals for ensuring that incorporation of AI into scientific research supports human values.