Four of the 11 projects on the shortlist are based at the University of Auckland.
Most of the short-listed projects for the fund, which is directed at biotechnology, information and communications technology (ICT) and "creative industries", have a biotechnology focus.
The Auckland University of Technology, which submitted two joint applications with other universities, has missed out.
"All this talk about ICT and there's basically nothing on the list at all," deputy vice chancellor of research Philip Sallis said.
A final choice will be made on March 4.
The shortlisted applicants are:
Allan Wilson Centre for Molecular Ecology and Evolution, based at Massey University;
Centre for Advanced Bio-protection Technologies, based at Lincoln University;
Centre for Molecular Biodiscovery, based at the University of Auckland;
Gateway Antarctica: Centre for Antarctic Studies and Research, based at the University of Canterbury;
MacDiarmid Institute for Advanced Materials and Nanotechnology, based at Victoria University;
Genes, Enzymes, Microbes Biotechnology Centre of Research Excellence, based at Waikato University;
Institute of Mathematics and its Applications, Auckland;
Public Health Research Institute, based at the University of Otago;
National Institute of Research Excellence for Maori Development and Advancement, Auckland;
Perinatal Systems Biology, Auckland; Riddett Centre, Massey.
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