The former Conservative politician was pictured in the Mirror newspaper browsing the shelves at a newsagents in west London on Tuesday.
Face coverings have been mandatory in shops, supermarkets and shopping centres across England since 24 July - a requirement brought in by Boris Johnson.
The picture emerged after fines increased to £200 last week for first time offenders who fail to wear a face covering in accordance with the guidance.
Speaking to the Mirror, Stanley Johnson admitted he may not be "100% up to speed” with current rules as he had just returned to England after three weeks abroad.
"I’m extremely sorry for the slip up and I would urge absolutely everybody to do everything they can to make sure they do follow the rules about masks and social distancing," he said.
"The fact this was my first day back in the UK after three weeks abroad is, I am sure, no excuse for not knowing the rules."
During the Downing Street press conference on Wednesday, the prime minister implored the public to follow coronavirus guidelines.
“Bear in mind that the fines are now very considerable and they will be imposed,” he said.
It is not the first time the prime minister’s father has made headlines – in July he defended his decision to travel to Greece in an apparent breach of Foreign Office guidance to avoid non-essential travel.
He admitted breaking lockdown rules when he went out to buy a newspaper after his grandchild was born in April, stating he was “not sure it’s an essential journey”, and also indicated in March that he would ignore the government’s advice and go to the pub.
Last week the government guidance on face masks was extended to hospitality venues, theatres, restaurants, bars and pubs unless people need to remove them to eat or drink.