The 80-year-old left the Albert Einstein hospital on Tuesday following successful surgery to remove a tumour in his colon earlier in September.
However, on Friday evening, ESPN Brasil reported that his condition has deteriorated due to acid reflux and he is now back in intensive care.
The football icon took to Instagram to provide an update on his condition.
"My friends, I am still recovering very well. Today I received visits from family members and I continue to smile every day. Thank you for all the love I get from you," Pele said on Instagram.
His daughter, Kely Nascimento, said her father was 'recovering well' in a statement on her Instagram account.
"Hi friends. I don't know what is going on with the rumours out there, but my DMs are booming!!! There's already a lot of anxiety roaming the world these days and we don't want to be the reason for more," Nascimento wrote on Instagram.
"This photo was taken just now. He is wearing a vest because he is Santista and the cold in SP (Sao Paulo) bothers him!
"He is recovering well and within normal range. Promise! The normal recovery scenario for a man of his age, after an operation like this, is sometimes two steps forward and one step back.
"Yesterday he was tired and took a little step back. Today he took two forwards!
"I want to thank again, and always, the brilliant team here at Einstein and even more gratitude for all of the good energy that you are transmitting."
Perhaps football's first world superstar, Pele rose to international prominence when he helped Brazil win the 1958 World Cup as a 17-year-old, repeating the feat in 1962 and 1970.
Officially, he scored 757 goals during a glittering career - club Santos claim his tally was closer to 1,000 - leaving him behind only Cristiano Ronaldo and Josef Biscan on the all-time list.