Tory MP John Penrose said he was alerted by the app, part of the operation overseen by his wife.
The Weston-super-Mare MP said on Twitter: "It never rains but it pours... my NHS app has just gone off, telling me to self-isolate, which I'm doing."
Lady Harding has not been told to self-isolate, Mr Penrose said.
People are told to self-isolate after potentially coming into contact with someone who has coronavirus.
It never rains but it pours.... my NHS app has just gone off, telling me to self-isolate, which I'm doing. No symptoms so far *crosses fingers*
— John Penrose (@JohnPenroseNews) November 9, 2020
Mr Penrose said on Twitter that he had no symptoms as yet.
Asked if he had spoken to his wife about it, he told the Press Association: "We are trying to make sure we are doing it by the book, if I can put it that way.
"Her NHS app has not gone off, so it's someone I have been in contact with rather than her."
In response to a suggestion that it showed the system worked, Mr Penrose said: "I suppose it does."
The contact-tracing scheme was launched to reduce the spread of coronavirus