But he told the BBC's Network Africa programme that getting a clearer idea of the number of gay people would be a huge help with targeted interventions such as provision of condoms.
He said the survey would involve gay men identifying each other, and officials carrying out HIV tests and providing along with information on safe sexual practice.
"Kenyans cannot actually afford to say that the gay community are isolated somewhere in the corner - they are part of our lives," he said.
"This group must be reached with information and services so they know how to protect themselves from getting infected."
Census first
Analysts say Kenya has made progress in its fight against HIV/Aids - one-in-10 people had the virus in the late 1990s, a rate that has now fallen to 6%.
Bookmark with:
What are these?