Thomson was first recommended to carry out two figure subjects for the Ministry of Supply, in March 1940, at £50 each. This led to further commissions for different Ministries, some of them through the Ministry of Information and some direct. One suggestion was that he should paint Alderman Halliwell of Coventry, (a commission that was also offered to Francis Dodd) but because of the bombing of that city, Halliwell postponed the portrait. Letters around (49) discuss the portrait of Charity Bick (IWM:ART LD 1207).
In October 1942, Thomson was offered a six-month salaried commission (£325) as an Air Ministry artist, replacing Kennington, who had resigned. However there is little detail of the work involved in this commission. By December 1943 both the Ministry and Clark seemed to be unhappy with his work (131), but there is no detail on this file of the termination of the contract.
Other correspondence concerns expenses, discussion of whether Thomson could exhibit his work at the Royal Academy shows (he was an Academician); requests for permits, photographs of works etc, after his official work had ended; and enquiries from the public, including requests from sitters and their families for photographic prints.