Cumulative funds for the three agencies rose to $13.1 billion; a 4.4 percent increase from 2012.
R&D funding for DHS rose 26.3 percent to $729 million.
The White House said funds will support advances in cybersecurity, explosives detection and response systems for chemical and biological threats.
The Energy Department would receive $11.9 billion for R&D, an 8 percent increase from 2012.
DOE will focus on developing clean energy technology and programs.
NIST’s R&D funding totals $708 million; a 13.8 percent increase from 2012.
The White House said the increase would go toward programs for advanced manufacturing, cybersecurity and nanotechnology.
Total defense R&D funding totals $71.2 billion; down $1.5 billion from fiscal 2012.
Non-defense R&D funding rose to $64.9 billion; up 5 percent from fiscal 2012.
Other agencies that saw proposed R&D increases for 2013 include:
- Environmental Protection Agency, up 2.1 percent to $580 million
- U.S. Geological Survey, 6.4 percent to $718 million
- NASA, up 2.2 percent to $9.6 billion
- National Nanotechnology Initiative, up 4.1 percent to $1.8 billion