The letter, issued earlier this week, said that housing associations are reviewing their existing financial commitments following the Budget 2015 announcement of reductions in social rents in the four years from 2016-17.
"As a result some approved or emerging schemes where housing associations are engaged with house builders through Section 106 agreements are not being built out at the anticipated rate. Delay risks planned homes not coming forward and the ability of councils being able to demonstrate a five-year supply of deliverable housing land", the letter said.
Lewis urged councils to "respond constructively, rapidly and positively to requests for such renegotiations and to take a pragmatic and proportionate approach to viability."
"Where it is simply proposed that the tenure mix is adjusted, with the overall affordable housing contribution remaining the same, it is our view that this is unlikely to justify reopening viability by either side. We would ask local authorities to expedite such renegotiations so they can be dealt with in a timely manner, and avoid action which might result in unnecessary delay.
"Should there be a need to reduce the overall amount of affordable housing, we strongly encourage local authorities to seek the minimum amount of viability information necessary, for example only that information which compares the financial position immediately prior to the Budget to the current position to justify the requested change."
The letter said that the government intends to introduce a dispute resolution mechanism to help speed up Section 106 negotiations and is to produce guidance on encouraging flexibility in renegotiating Section 106 deals.
It also said that Lewis would be contacting local authorities over the next few weeks "to understand the extent to which they are being approached to renegotiate Section 106 Agreements, and what action authorities are taking."