The pontiff had to leave four hours ahead of schedule and told the crowd at the main cathedral in Leyte province he was "sad" about it.
"I apologise to all of you," he said.
"I am sad about this, truly saddened, because I had something prepared especially for you."
Francis was due to meet survivors of Typhoon Haiyan, which battered the Philippines just over a year ago.
He was given a wood image of Our Lady of Immaculate Conception that was made using the debris from a damaged church.
The Holy Father also said mass for tens of thousands of people during high winds and heavy rain.
Many of the worshippers had spent hours in the bad weather to get a good view of the Pope.
He conceded that it was hard to find the right words when surrounded by so much pain.
"So many of you have lost everything," he told the congregation of around 150,000 Catholics.
"I don't know what to say to you, but the Lord does know what to say to you. Some of you lost part of your families. All I can do is keep silent. And I walk with you all with my silent heart."
He told the crowds he decided to come to the Philippines in the immediate aftermath of last year's typhoon: "I wanted to come to be with you. It's a bit late, I have to say, but I am here," he said.
In traditional Francis style he did not use his prepared homily and instead spoke about the pain felt by those suffering in the aftermath of the typhoon: "Thank you, Lord, for sharing our pain. Thank you, Lord, for giving us hope."
Filipino Faith is priceless, typhoon are no match! #PapalVisitPH #popefrancisph pic.twitter.com/MRMkXw11wF
— Papal Visit 2015 (@papalvisitph) January 17, 2015