In and since 1856, successive attempts were made to sell the English Church to Government and to secure its conversion into a Government Chaplaincy. This was because, on one hand, the Directors, feeling that Governments in India ought to dissociate themselves from missionary work, had already embarked on a definite policy of abolishing the joint use of Churches by European and Indian congregations, not only in San Thome but also in ‘Black Town’, Trichinopoly, Tanjore, Ramnad, Palayamcottai and Chittoor. On the other hand, the Bishop, the Archdeacon and the S.P.G. were convinced that it was not morally right to expend Mission funds on European congregations.
It must be remembered that, at this time, St. Thomas was the fashionable Church of Madras and was attended by the Governor of Madras (who held a pew) and by the elite of Madras Society, who also, incidentally, contributed liberally towards S.P.G. Funds. The Church building, therefore, together with the School and the Parsonage, was offered to the Government and was valued by the chief Engineer at Rs. 20,068. But the sale was never effected for one reason or another. All that happened was that a grant of Rs. 100 per month was obtained in 1863 from Government of ministerial services to the English congregation and for the use of the burial ground, the Government also undertaking to keep the fabric in repair for the time being.
For many years since, the incumbency of the church was filled by the Secretaries of the S.P.G., Madras, notably by A.R. Symonds, J.M. Strachan, M.D., afterwards Bishop of Rangoon, C.E. Kennet, D.D. (Lambeth), the Anglo-Indian divine, F.H. Reichardt, W. Relton and Arthur Westcott. The Church was also served by Principals of St. Paul’s High School, Vepery, namely, the Rev. K.V. McPherson, and by the Rev. G.M. Withers and by Cathedral Chaplains. Rev. David Chellappa (who later on became the second Bishop of Madras Diocese when the Church of South India was formed) was the first Indian to serve here. There are about 12 memorial tablets of congregation members from this period.