The biggest weapons that the government has are funding and policy. Scientific research requires resources and in turn, money. Governments spend billions of dollar each year on research, in various disciplines. For example, National Science Foundation (NSF), National Institute of Health (NIH), Department of Energy (DoE), etc. are some of the governmental organizations who fund research in United States. The government can decide on some focus areas (say, infrastructural development and cancer research or fuel cell and batteries, etc.) and channel more funds into those areas. This will result in more research in these areas, while drying up funds from other areas and reducing the amount of research in them. The government can also make policy changes, such as banning stem cell research, etc., that will change the direction of scientific research in some disciplines.
Hope this helps.