The Sunday Mail first reported that Strathclyde Partnership for Transport (SPT) head Gordon Maclennan had two VW Passats with identical registration plates.
The newspaper published photographs it said showed one vehicle in a staff car park and another at his holiday home in the Isle of Lewis.
Mr Maclennan denied any wrongdoing but was suspended by SPT while an investigation was carried out.
SPT runs the Glasgow Subway as well as subsidised bus services in and around the city.
A spokeswoman for the organisation said the transport head has now retired.
“Mr Gordon Maclennan, 72, has informed the SPT chair, Cllr Dr Martin Bartos, that he wishes to retire with immediate effect,” she said.
“This has been accepted and SPT thank Mr Maclennan for his many years of service.”
In regards to the investigation, she added: “SPT will continue to review matters where there are issues pertaining to SPT.”
In a statement on his retirement, Mr Maclennan said: “It has been a privilege to lead SPT over the past 10 years and as I retire, I wish my colleagues continued success in assisting the citizens of Strathclyde in addressing the changing transport requirements.”
The Sunday Mail published a photograph appearing to show Mr Maclennan entering a silver Passat on Lewis. Another photograph showed a blue Passat with an identical registration plate outside the SPT headquarters in Glasgow.
Cloning a registration plate is illegal, as cloned cars could escape paying tax, insurance and MoT costs.