A spokesman said Francis would continue with the rest of his day’s business, but preferred to stay within the Vatican rather than travel across the city.
There was no word from the Vatican about the nature of his illness, but the pope was seen coughing and blowing his nose during the Ash Wednesday Mass.
It comes a day after he kissed heads and touched faces as he met with crowds in St Peter’s Square, saying he had solidarity with those suffering from coronavirus.
Italy is currently in the grips of a coronavirus outbreak that has seen towns in the north placed on lockdown and travelers from the region spread the infection to previously unaffected areas of Europe.
Rome had three cases, but all three were cured.
Francis had been scheduled to go to the St John Lateran basilica to meet with Rome clergy and celebrate a penitential Mass at the start of Lent.
Francis is a bishop of Rome but delegates the day-to-day running of the archdiocese to a vicar.
The Argentine pope has generally enjoyed good health. He lost part of one lung as a young man because of respiratory illness and suffers from sciatica, which makes walking difficult.
Francis has had a busy schedule lately, including his public general audience on Wednesday and the Ash Wednesday service later in the day in a Roman basilica.
Only a few of the 12,000 or so faithful who turned out to see him on Saint Peter’s Square were wearing face masks.
But the 83-year-old Francis did not shy away from shaking hands with members of the congregation – and even kissed some of the children present.
Pope Francis is known to hug the faithful or accepting kisses on his cheek or forehead.
However, a year ago he explained his reticence for allowing people to kiss his ring, explaining the practice could spread germs.
In his Ash Wednesday homily marking the beginning of Lent, the pope exhorted the world’s 1.3 billion Catholics to ‘switch off the television and open the Bible’.
He urged followers to give up trolling people on social media platforms like Twitter and Facebook for Lent.
He said there was too much ‘verbal violence’ in the world which was ‘amplified by the internet’.
Francis added that Lent was ‘a time to give up useless words, gossip, rumors, tittle-tattle and speak to God on a first name basis.’
It comes as 50 more cases – including eight children – of COVID-19 have now been confirmed in Italy, taking the toll past 370. Twelve patients have died.
Almost a dozen towns have been quarantined in the northern part of the country in a desperate attempt to contain the worsening coronavirus crisis.
It comes after thousands of British families jetted to Italy during the half-term break from schools last week and Easter holidays are just five weeks away.
More than 82,000 cases of the COVID-19 – the disease caused by the coronavirus – have been recorded across the world, with the death toll nearing 2,800.