An alleged victim told police he was assaulted when he was 16 or 17 on a train between Newport, south Wales, and London Paddington.
This follows earlier complaints made against the Port Talbot born Cardiff MP who died in 1997.
BTP said it had been made aware of "inappropriate touching" allegations.
A spokesman said: "BTP was made aware of an allegation of inappropriate touching involving the late George Thomas on board a train from London Paddington to Aberystwyth in 1959.
"I can confirm that a second report has been received, from Gwent Police, involving allegations of a sexual assault during a train journey from Newport to London Paddington between 1964 and 1966.
"The complainant, who was aged 16 or 17 at the time, did not wish to make a formal statement to police.
"The information has since been passed to the Operation Hydrant investigating team."
Operation Hydrant teams are gathering evidence for a number of investigations into historical child sexual abuse allegations, including Operation Pallial in north Wales and Operation Yewtree, the inquiry prompted by the Jimmy Savile abuse cases.
A second set of sex abuse allegations have been made against former House of Commons Speaker George Thomas,  British Transport Police (BTP) has confirmed.