On 30 January 1984 Thomas was convicted at Gowerton Magistrates' Court, Swansea, of importuning for immoral purposes at a men's public lavatory (he was fined £75). The case was reported and attracted negative publicity for Thomas, who announced to Carmarthen Constituency Labour Party on 2 March that he would resign his seat. He subsequently delayed his resignation, after pressure from within the party.

In the meantime, Thomas continued his Parliamentary activity and remained one of the most active Welsh MPs of all. He also received a good deal of sympathy on his plight, and times had moved on since William Field was forced to resign in similar circumstances thirty years before. A similar scandal involving the Conservative MP Keith Hampson deflected some attention. Thomas was pressed to stay on by the Labour whips, who feared the loss of the marginal seat in a by-election.

On 17 August he announced he would remain until the dissolution of Parliament.