The 86-year-old pope skipped reading a key speech that was on the programme of his two-hour visit to the world-famous shrine north of Lisbon.
The omission did not appear to indicate that the pope was experiencing any health issues. He later greeted dozens of people individually as an aide slowly pushed his wheelchair through the crowd.
He stopped often to often to kiss babies and comfort the sick as he made his way back to a helicopter transporting him to the next event on his five-day trip to Portugal.
Vatican spokesman Matteo Bruni said the pope's apparently last-minute decision to skip the speech, which was expected to have been the centrepiece of the day, did not appear to have anything to do with Francis' eyesight.
He has shortened several speeches or has chosen to speak instead off-script since the trip started on Wednesday. He said on one occasion that he was having trouble with his glasses.
"The pope always addresses firstly the people he meets, as a shepherd, and speaks accordingly," Bruni said in response to questions from reporters.
Francis flew in from Lisbon - the venue of a Catholic youth festival - to make his second visit as pope to the shrine that draws millions of pilgrims a year.
At the start of his visit a smoke cloud caused by a wild fire at Castelo Branco, about 100 km (60 miles) east of Fatima, hovered over one side of the sanctuary and tiny specks of ash fell. It later mostly dissipated.
SECRETS OF FATIMA
Fatima has captivated Catholics since the children's first reported vision of the Virgin Mary on May 13, 1917.
Siblings Francisco and Jacinta Marto died several years later and were declared saints in 2017. The third, Lucia Dos Santos, became a nun and died in 2005 at the age of 97. Efforts are underway to make her a saint too.
The children said the Madonna gave them three messages, the so-called Secrets of Fatima.
The first two were revealed soon after and concerned a vision of hell, seen by believers as a prediction of the outbreak of World War Two, a warning that Russia would "spread her errors" in the world, and a need for general conversion to God and prayer.
The third was known only to Sister Lucia and popes and it intrigued the world for more than three-quarters of a century, inspiring books and cults convinced it was the timing of the end of the world.
In 2000, the Vatican said it was a prediction of the 1981 assassination attempt on Pope John Paul on May 13, the same day of the first reported apparition in 1917.
(Reporting by Catarina Demony, Philip Pullella, Michael Gore and Pedro Nunes;Editing by Andrew Cawthorne and Frances Kerry)
By Philip Pullella and Catarina Demony
