The heir to the throne, who also is the duke of Cambridge, has been flying Sea Kings at RAF Valley in Anglesey since 2010. The newspaper said the prince and his wife, the former Kate Middleton, who had been living in a house on an estate on Anglesey, will now split their time between Kensington Palace in London and a house on the royal estate at Sandringham in Norfolk.
The couple are expecting their first child in July.
William told his commander this is the time for him to "move on," the Times said. The newspaper said he might take up other military duties.
While the duke and duchess have carried out royal duties, they generally lived a quiet life while in Anglesey on the Bodorgan estate owned by Sir George and Lady Meyrick.