A minister has revealed that 490 beggars and homeless people were sent to a luxury holiday retreat for the January 15-19 visit.
After the Pope had left they were sent back to live on the streets, Social Welfare Secretary Corazon Soliman said.
Members of parliament demanded an explanation. House of Representatives member Terry Ridon told AFP: "The pope would have wanted to see the Philippines, warts and all. Let us not pretend that we are a first-world country."
The government was also accused of "whitewashing poverty" after removing the people before the Pope held an open air mass for a record six million crowd.
But the minister responded by saying the homeless would have been "vulnerable to syndicates and discriminated [against] a lot".
"You cannot hide poverty. When the pope landed, the first thing he saw was the shanties by the river," she told AFP.
It's been reported that the hotel the homeless were sent to cost around £370 a night.