The warning comes in the commission's new Affordable Home Ownership – Charitable Status and Tax document, published in collaboration with HM Revenue & Customs and social housing regulator the Housing Corporation.
The document sets out when providing low-cost home ownership is charitable, and warns that government priorities for affordable housing are not necessarily charitable.
It says providing housing can serve various charitable purposes, such as relieving need, promoting urban regeneration and helping the elderly or disabled. It says providing housing for key workers such as teachers or nurses can also be charitable.
The document also explains how to assess who can benefit from low cost housing schemes, and offers advice on the tax implications of different kinds of trading activity.